############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL IgGeneUsage ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘IgGeneUsage’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++17 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_dgu.cc -o stanExports_dgu.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/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_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector > stan::io::dump::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) { | ~~~~^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector > stan::io::random_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector > stan::io::array_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu.h:11, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = double; Eigen::Index = long int]’: stanExports_dgu.h:673:35: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long unsigned int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_dgu.cc:5: stanExports_dgu.h: In instantiation of ‘void model_dgu_namespace::model_dgu::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu.h:1477:36: required from here stanExports_dgu.h:925:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 925 | int pos__ = std::numeric_limits::min(); | ^~~~~ stanExports_dgu.h: In instantiation of ‘void model_dgu_namespace::model_dgu::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu.h:1487:36: required from here stanExports_dgu.h:925:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’: stanExports_dgu.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 207 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 208 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t* = 0; Idxs = {}]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare] 39 | if (unlikely(!(y <= high))) { | ~~~^~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’ 9 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_dgu_namespace::model_dgu; Eigen::MatrixXd = Eigen::Matrix]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 55 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 71 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector; Real = long double; Policy = boost::math::policies::policy; Terminal = boost::math::detail::iteration_terminator]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector; Real = double; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector; Tb = std::vector; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 122 | std::pair hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu.h:11, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector, -1, 1>, std::allocator, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = stan::math::var_value; Eigen::Index = long int]’: stanExports_dgu.h:496:79: required from ‘stan::scalar_type_t model_dgu_namespace::model_dgu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu.h:1450:47: required from ‘T_ model_dgu_namespace::model_dgu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_namespace::model_dgu; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder::temme_root_finder(T, T) [with T = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 793 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Array; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu.h:561:54: required from ‘stan::scalar_type_t model_dgu_namespace::model_dgu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu.h:1450:47: required from ‘T_ model_dgu_namespace::model_dgu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_namespace::model_dgu; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan, -1, 1> >::; T = Eigen::Matrix, -1, 1>; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix, -1, 1>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu.h:565:60: required from ‘stan::scalar_type_t model_dgu_namespace::model_dgu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu.h:1450:47: required from ‘T_ model_dgu_namespace::model_dgu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_namespace::model_dgu; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan > >::; T = Eigen::ArrayWrapper >; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper >]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = double]’ stanExports_dgu.h:561:54: required from ‘stan::scalar_type_t model_dgu_namespace::model_dgu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = double; std::ostream = std::basic_ostream]’ stanExports_dgu.h:1450:47: required from ‘T_ model_dgu_namespace::model_dgu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_dgu_namespace::model_dgu; bool jacobian = false]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector&, const std::vector >&, RNG_t&) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit::call_sampler(SEXP) [with Model = model_dgu_namespace::model_dgu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu.cc:15:87: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 61 | std::pair r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations()), scale); | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu.h:9, from stanExports_dgu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_dgu_paired.cc -o stanExports_dgu_paired.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/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_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector > stan::io::dump::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) { | ~~~~^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector > stan::io::random_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector > stan::io::array_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu_paired.h:11, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = double; Eigen::Index = long int]’: stanExports_dgu_paired.h:712:34: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long unsigned int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_dgu_paired.cc:5: stanExports_dgu_paired.h: In instantiation of ‘void model_dgu_paired_namespace::model_dgu_paired::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu_paired.h:1540:36: required from here stanExports_dgu_paired.h:975:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 975 | int pos__ = std::numeric_limits::min(); | ^~~~~ stanExports_dgu_paired.h: In instantiation of ‘void model_dgu_paired_namespace::model_dgu_paired::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu_paired.h:1550:36: required from here stanExports_dgu_paired.h:975:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’: stanExports_dgu_paired.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 207 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 208 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t* = 0; Idxs = {}]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare] 39 | if (unlikely(!(y <= high))) { | ~~~^~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’ 9 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_dgu_paired_namespace::model_dgu_paired; Eigen::MatrixXd = Eigen::Matrix]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 55 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 71 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector; Real = long double; Policy = boost::math::policies::policy; Terminal = boost::math::detail::iteration_terminator]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector; Real = double; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector; Tb = std::vector; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 122 | std::pair hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu_paired.h:11, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector, -1, 1>, std::allocator, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = stan::math::var_value; Eigen::Index = long int]’: stanExports_dgu_paired.h:523:78: required from ‘stan::scalar_type_t model_dgu_paired_namespace::model_dgu_paired::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_paired.h:1513:47: required from ‘T_ model_dgu_paired_namespace::model_dgu_paired::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_paired_namespace::model_dgu_paired; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder::temme_root_finder(T, T) [with T = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 793 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Array; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu_paired.h:598:54: required from ‘stan::scalar_type_t model_dgu_paired_namespace::model_dgu_paired::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_paired.h:1513:47: required from ‘T_ model_dgu_paired_namespace::model_dgu_paired::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_paired_namespace::model_dgu_paired; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan, -1, 1> >::; T = Eigen::Matrix, -1, 1>; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix, -1, 1>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu_paired.h:607:60: required from ‘stan::scalar_type_t model_dgu_paired_namespace::model_dgu_paired::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_paired.h:1513:47: required from ‘T_ model_dgu_paired_namespace::model_dgu_paired::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_paired_namespace::model_dgu_paired; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan > >::; T = Eigen::ArrayWrapper >; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper >]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = double]’ stanExports_dgu_paired.h:598:54: required from ‘stan::scalar_type_t model_dgu_paired_namespace::model_dgu_paired::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = double; std::ostream = std::basic_ostream]’ stanExports_dgu_paired.h:1513:47: required from ‘T_ model_dgu_paired_namespace::model_dgu_paired::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_dgu_paired_namespace::model_dgu_paired; bool jacobian = false]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector&, const std::vector >&, RNG_t&) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit::call_sampler(SEXP) [with Model = model_dgu_paired_namespace::model_dgu_paired; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired.cc:15:87: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 61 | std::pair r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations()), scale); | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired.h:9, from stanExports_dgu_paired.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_dgu_paired_rep.cc -o stanExports_dgu_paired_rep.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/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_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_paired_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector > stan::io::dump::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) { | ~~~~^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector > stan::io::random_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector > stan::io::array_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu_paired_rep.h:11, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = double; Eigen::Index = long int]’: stanExports_dgu_paired_rep.h:767:34: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long unsigned int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_dgu_paired_rep.cc:5: stanExports_dgu_paired_rep.h: In instantiation of ‘void model_dgu_paired_rep_namespace::model_dgu_paired_rep::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu_paired_rep.h:1716:36: required from here stanExports_dgu_paired_rep.h:1062:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 1062 | int pos__ = std::numeric_limits::min(); | ^~~~~ stanExports_dgu_paired_rep.h: In instantiation of ‘void model_dgu_paired_rep_namespace::model_dgu_paired_rep::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu_paired_rep.h:1726:36: required from here stanExports_dgu_paired_rep.h:1062:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’: stanExports_dgu_paired_rep.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 207 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 208 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t* = 0; Idxs = {}]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare] 39 | if (unlikely(!(y <= high))) { | ~~~^~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’ 9 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; Eigen::MatrixXd = Eigen::Matrix]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired_rep.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 55 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 71 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector; Real = long double; Policy = boost::math::policies::policy; Terminal = boost::math::detail::iteration_terminator]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector; Real = double; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector; Tb = std::vector; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 122 | std::pair hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu_paired_rep.h:11, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector, -1, 1>, std::allocator, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = stan::math::var_value; Eigen::Index = long int]’: stanExports_dgu_paired_rep.h:548:78: required from ‘stan::scalar_type_t model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_paired_rep.h:1689:47: required from ‘T_ model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_paired_rep_namespace::model_dgu_paired_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder::temme_root_finder(T, T) [with T = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 793 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Array; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu_paired_rep.h:642:54: required from ‘stan::scalar_type_t model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_paired_rep.h:1689:47: required from ‘T_ model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_paired_rep_namespace::model_dgu_paired_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan, -1, 1> >::; T = Eigen::Matrix, -1, 1>; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix, -1, 1>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu_paired_rep.h:651:60: required from ‘stan::scalar_type_t model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_paired_rep.h:1689:47: required from ‘T_ model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_paired_rep_namespace::model_dgu_paired_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan > >::; T = Eigen::ArrayWrapper >; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper >]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = double]’ stanExports_dgu_paired_rep.h:642:54: required from ‘stan::scalar_type_t model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = double; std::ostream = std::basic_ostream]’ stanExports_dgu_paired_rep.h:1689:47: required from ‘T_ model_dgu_paired_rep_namespace::model_dgu_paired_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; bool jacobian = false]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector&, const std::vector >&, RNG_t&) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit::call_sampler(SEXP) [with Model = model_dgu_paired_rep_namespace::model_dgu_paired_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_paired_rep.cc:15:87: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 61 | std::pair r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations()), scale); | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_paired_rep.h:9, from stanExports_dgu_paired_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_dgu_rep.cc -o stanExports_dgu_rep.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/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_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_dgu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector > stan::io::dump::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) { | ~~~~^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector > stan::io::random_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector > stan::io::array_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu_rep.h:11, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = double; Eigen::Index = long int]’: stanExports_dgu_rep.h:766:31: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long unsigned int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_dgu_rep.cc:5: stanExports_dgu_rep.h: In instantiation of ‘void model_dgu_rep_namespace::model_dgu_rep::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu_rep.h:1695:36: required from here stanExports_dgu_rep.h:1055:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 1055 | int pos__ = std::numeric_limits::min(); | ^~~~~ stanExports_dgu_rep.h: In instantiation of ‘void model_dgu_rep_namespace::model_dgu_rep::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_dgu_rep.h:1705:36: required from here stanExports_dgu_rep.h:1055:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’: stanExports_dgu_rep.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 207 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 208 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t* = 0; Idxs = {}]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare] 39 | if (unlikely(!(y <= high))) { | ~~~^~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’ 9 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_dgu_rep_namespace::model_dgu_rep; Eigen::MatrixXd = Eigen::Matrix]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_rep.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 55 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 71 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector; Real = long double; Policy = boost::math::policies::policy; Terminal = boost::math::detail::iteration_terminator]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector; Real = double; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector; Tb = std::vector; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 122 | std::pair hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_dgu_rep.h:11, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector, -1, 1>, std::allocator, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = stan::math::var_value; Eigen::Index = long int]’: stanExports_dgu_rep.h:551:75: required from ‘stan::scalar_type_t model_dgu_rep_namespace::model_dgu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_rep.h:1668:47: required from ‘T_ model_dgu_rep_namespace::model_dgu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_rep_namespace::model_dgu_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder::temme_root_finder(T, T) [with T = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 793 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Array; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu_rep.h:640:54: required from ‘stan::scalar_type_t model_dgu_rep_namespace::model_dgu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_rep.h:1668:47: required from ‘T_ model_dgu_rep_namespace::model_dgu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_rep_namespace::model_dgu_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan, -1, 1> >::; T = Eigen::Matrix, -1, 1>; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix, -1, 1>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_dgu_rep.h:644:60: required from ‘stan::scalar_type_t model_dgu_rep_namespace::model_dgu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_dgu_rep.h:1668:47: required from ‘T_ model_dgu_rep_namespace::model_dgu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_dgu_rep_namespace::model_dgu_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan > >::; T = Eigen::ArrayWrapper >; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper >]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = double]’ stanExports_dgu_rep.h:640:54: required from ‘stan::scalar_type_t model_dgu_rep_namespace::model_dgu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = double; std::ostream = std::basic_ostream]’ stanExports_dgu_rep.h:1668:47: required from ‘T_ model_dgu_rep_namespace::model_dgu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_dgu_rep_namespace::model_dgu_rep; bool jacobian = false]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector&, const std::vector >&, RNG_t&) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit::call_sampler(SEXP) [with Model = model_dgu_rep_namespace::model_dgu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_dgu_rep.cc:15:87: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 61 | std::pair r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations()), scale); | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_dgu_rep.h:9, from stanExports_dgu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_gu.cc -o stanExports_gu.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/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_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector > stan::io::dump::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) { | ~~~~^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector > stan::io::random_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector > stan::io::array_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_gu.h:11, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = double; Eigen::Index = long int]’: stanExports_gu.h:507:35: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long unsigned int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_gu.cc:5: stanExports_gu.h: In instantiation of ‘void model_gu_namespace::model_gu::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_gu.h:1041:36: required from here stanExports_gu.h:670:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 670 | int pos__ = std::numeric_limits::min(); | ^~~~~ stanExports_gu.h: In instantiation of ‘void model_gu_namespace::model_gu::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_gu.h:1051:36: required from here stanExports_gu.h:670:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’: stanExports_gu.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 207 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 208 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t* = 0; Idxs = {}]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare] 39 | if (unlikely(!(y <= high))) { | ~~~^~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’ 9 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_gu_namespace::model_gu; Eigen::MatrixXd = Eigen::Matrix]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 55 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 71 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector; Real = long double; Policy = boost::math::policies::policy; Terminal = boost::math::detail::iteration_terminator]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector; Real = double; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector; Tb = std::vector; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 122 | std::pair hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_gu.h:11, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector, -1, 1>, std::allocator, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = stan::math::var_value; Eigen::Index = long int]’: stanExports_gu.h:381:79: required from ‘stan::scalar_type_t model_gu_namespace::model_gu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_gu.h:1014:47: required from ‘T_ model_gu_namespace::model_gu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_gu_namespace::model_gu; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder::temme_root_finder(T, T) [with T = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 793 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Array; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_gu.h:420:54: required from ‘stan::scalar_type_t model_gu_namespace::model_gu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_gu.h:1014:47: required from ‘T_ model_gu_namespace::model_gu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_gu_namespace::model_gu; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan, -1, 1> >::; T = Eigen::Matrix, -1, 1>; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix, -1, 1>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_gu.h:425:60: required from ‘stan::scalar_type_t model_gu_namespace::model_gu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_gu.h:1014:47: required from ‘T_ model_gu_namespace::model_gu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_gu_namespace::model_gu; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan > >::; T = Eigen::ArrayWrapper >; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper >]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = double]’ stanExports_gu.h:420:54: required from ‘stan::scalar_type_t model_gu_namespace::model_gu::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = double; std::ostream = std::basic_ostream]’ stanExports_gu.h:1014:47: required from ‘T_ model_gu_namespace::model_gu::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_gu_namespace::model_gu; bool jacobian = false]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector&, const std::vector >&, RNG_t&) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit::call_sampler(SEXP) [with Model = model_gu_namespace::model_gu; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu.cc:15:87: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 61 | std::pair r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations()), scale); | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu.h:9, from stanExports_gu.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_gu_rep.cc -o stanExports_gu_rep.o In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 251 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 508 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 521 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 604 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 613 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 615 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector&, const int&, const int&, const int&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 73 | for (std::size_t i = 0; i < p - 1; i++) { | ~~^~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 79 | } while (k < x); | ~~^~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 105 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector&, const int&, const double&, const std::vector&, std::vector&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 126 | for (std::size_t j = 0; j != k; j++) { | ~~^~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 132 | while ((first_zero < index.size()) && index[first_zero]) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | if (first_zero == index.size()) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 143 | for (std::size_t i = 0; i != first_zero + 1; i++) { | ~~^~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector >&)’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) { | ~~^~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/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_::************ | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41, from /usr/include/c++/10.3.1/locale:43, from /usr/include/c++/10.3.1/iomanip:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27, from stanExports_gu_rep.cc:3: /usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector > stan::io::dump::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 85 | for (Eigen::Index pos = 0; pos < l_tri_size; pos++) { | ~~~~^~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector > stan::io::random_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector > stan::io::array_var_context::vals_c(const string&) const’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 317 | real_iter < val_i->second.first.size(); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_gu_rep.h:11, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = double; Eigen::Index = long int]’: stanExports_gu_rep.h:602:31: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long unsigned int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 74 | for (int i = 0; i < dims.size(); i++) { | ~~^~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] In file included from stanExports_gu_rep.cc:5: stanExports_gu_rep.h: In instantiation of ‘void model_gu_rep_namespace::model_gu_rep::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_gu_rep.h:1259:36: required from here stanExports_gu_rep.h:802:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] 802 | int pos__ = std::numeric_limits::min(); | ^~~~~ stanExports_gu_rep.h: In instantiation of ‘void model_gu_rep_namespace::model_gu_rep::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix; VecI = std::vector; stan::require_vector_t* = 0; stan::require_vector_like_vt* = 0; std::ostream = std::basic_ostream]’: stanExports_gu_rep.h:1269:36: required from here stanExports_gu_rep.h:802:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’: stanExports_gu_rep.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 1252 | int ret = stan::services::error_codes::CONFIG; | ^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 207 | for (size_t i = 0; i < x.rows(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 208 | for (size_t j = 0; j < x.cols(); j++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t* = 0; Idxs = {}]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector stan::io::array_var_context::validate_dims(const std::vector >&, T, const std::vector >&) [with T = long int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare] 39 | if (unlikely(!(y <= high))) { | ~~~^~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’ 9 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_gu_rep_namespace::model_gu_rep; Eigen::MatrixXd = Eigen::Matrix]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit::standalone_gqs(SEXP, SEXP) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu_rep.cc:30:89: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 55 | if (p_names.size() != draws.cols()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 71 | for (size_t i = 0; i < draws.rows(); ++i) { | ~~^~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector; Real = long double; Policy = boost::math::policies::policy; Terminal = boost::math::detail::iteration_terminator]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35: required from ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector; Real = double; typename boost::math::tools::promote_args::type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28: required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector; Tb = std::vector; Tz = double; stan::require_all_vector_t* = 0; stan::require_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28: required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 122 | std::pair hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:6, from stanExports_gu_rep.h:11, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp: In instantiation of ‘auto stan::io::deserializer::read(Eigen::Index, Sizes ...) [with Ret = std::vector, -1, 1>, std::allocator, -1, 1> > >; Sizes = {int}; stan::require_std_vector_t* = 0; stan::require_not_same_t::type, T>* = 0; T = stan::math::var_value; Eigen::Index = long int]’: stanExports_gu_rep.h:438:75: required from ‘stan::scalar_type_t model_gu_rep_namespace::model_gu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_gu_rep.h:1232:47: required from ‘T_ model_gu_rep_namespace::model_gu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_gu_rep_namespace::model_gu_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:337:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 337 | for (size_t i = 0; i < m; ++i) { | ~~^~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Matrix; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix; Tb = Eigen::Matrix; Tz = double; stan::require_all_eigen_st* = 0; stan::require_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional; stan::require_all_arithmetic_t* = 0; stan::return_type_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t >* = 0]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder::temme_root_finder(T, T) [with T = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48: required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20: required from ‘boost::math::tools::promote_args_t boost::math::ibeta_inv(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable] 29 | const T x_extrema = 1 / (1 + a); | ^~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract::result_type boost::math::detail::upper_incomplete_gamma_fract::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35: required from ‘boost::math::tools::promote_args_t boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 299 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘boost::math::tools::promote_args_t boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 543 | std::pair owens_t_T1_accelerated(T h, T a, const Policy& pol) | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t::result_type = std::pair]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double; uintmax_t = long unsigned int]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = double; typename boost::math::tools::detail::fraction_traits::result_type = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93: required from ‘boost::math::tools::promote_args_t boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; boost::math::tools::promote_args_t = double]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 793 | result_type operator()() | ^~~~~~~~ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan >::; T = Eigen::Array; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_gu_rep.h:501:54: required from ‘stan::scalar_type_t model_gu_rep_namespace::model_gu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_gu_rep.h:1232:47: required from ‘T_ model_gu_rep_namespace::model_gu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_gu_rep_namespace::model_gu_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 153 | for (size_t i = 0; i < x.size(); i++) { | ~~^~~~~~~~~~ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan, -1, 1> >::; T = Eigen::Matrix, -1, 1>; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix, -1, 1>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/std_normal_lpdf.hpp:37:16: required from ‘stan::return_type_t stan::math::std_normal_lpdf(const T_y&) [with bool propto = false; T_y = Eigen::Matrix, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = stan::math::var_value]’ stanExports_gu_rep.h:506:60: required from ‘stan::scalar_type_t model_gu_rep_namespace::model_gu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector, std::allocator > >; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = stan::math::var_value; std::ostream = std::basic_ostream]’ stanExports_gu_rep.h:1232:47: required from ‘T_ model_gu_rep_namespace::model_gu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector&, std::vector&, std::vector&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_gu_rep_namespace::model_gu_rep; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit::grad_log_prob(SEXP, SEXP) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu_rep.cc:23:88: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare] /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan > >::; T = Eigen::ArrayWrapper >; Indexings = {}; stan::require_eigen_t* = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* = 0]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper >]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t* = 0; stan::return_type_t = double]’ stanExports_gu_rep.h:501:54: required from ‘stan::scalar_type_t model_gu_rep_namespace::model_gu_rep::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector; VecI = std::vector; stan::require_vector_like_t* = 0; stan::require_vector_like_vt* = 0; stan::scalar_type_t = double; std::ostream = std::basic_ostream]’ stanExports_gu_rep.h:1232:47: required from ‘T_ model_gu_rep_namespace::model_gu_rep::log_prob(std::vector&, std::vector&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_gu_rep_namespace::model_gu_rep; bool jacobian = false]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector&, const std::vector >&, RNG_t&) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; Rcpp::List = Rcpp::Vector<19>]’ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit::call_sampler(SEXP) [with Model = model_gu_rep_namespace::model_gu_rep; RNG_t = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >; SEXP = SEXPREC*]’ stanExports_gu_rep.cc:15:87: required from here /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase > >::Index’ {aka ‘long int’} [-Wsign-compare] In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector; Real = double; Policy = boost::math::policies::policy]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 61 | std::pair r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations()), scale); | ^ In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43, from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4, from stanExports_gu_rep.h:9, from stanExports_gu_rep.cc:5: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o IgGeneUsage.so RcppExports.o stanExports_dgu.o stanExports_dgu_paired.o stanExports_dgu_paired_rep.o stanExports_dgu_rep.o stanExports_gu.o stanExports_gu_rep.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-IgGeneUsage/00new/IgGeneUsage/libs ** R ** data ** 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 (IgGeneUsage)