##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL genphen
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘genphen’ ...
** libs
"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan
Wrote C++ file "stan_files/H.cc"
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c stan_files/H.cc -o stan_files/H.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:44,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:325,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/H.hpp:18,
from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
static void set_zero_all_adjoints() {
^
"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan
Wrote C++ file "stan_files/U.cc"
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c stan_files/U.cc -o stan_files/U.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> & r )
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr<Y> && r )
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:44,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:325,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
template<class T> T * get_pointer(std::auto_ptr<T> const& p)
^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
from /usr/include/c++/5/locale:43,
from /usr/include/c++/5/iomanip:43,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
template<typename> class auto_ptr;
^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
from stan_files/U.hpp:18,
from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
static void set_zero_all_adjoints() {
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o genphen.so stan_files/H.o stan_files/U.o init.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
rm stan_files/H.cc stan_files/U.cc
installing to /home/biocbuild/bbs-3.8-bioc/R/library/genphen/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
* DONE (genphen)
