* installing *source* package ‘rstanarm’ ... ** package ‘rstanarm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.4’ using C++17 make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rstanarm/src' "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan Wrote C++ file "stan_files/bernoulli.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/bernoulli.cc -o stan_files/bernoulli.o In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/bernoulli.cc:3: stan_files/bernoulli.hpp:5321:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 5321 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/bernoulli.cc:3: In file included from stan_files/bernoulli.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 19 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/binomial.stan Wrote C++ file "stan_files/binomial.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/binomial.cc -o stan_files/binomial.o In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/binomial.cc:3: stan_files/binomial.hpp:4114:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 4114 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/binomial.cc:3: In file included from stan_files/binomial.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 19 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/continuous.stan Wrote C++ file "stan_files/continuous.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/continuous.cc -o stan_files/continuous.o In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/continuous.cc:3: stan_files/continuous.hpp:8196:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 8196 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/continuous.cc:3: In file included from stan_files/continuous.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 19 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/count.stan Wrote C++ file "stan_files/count.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/count.cc -o stan_files/count.o In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/count.cc:3: stan_files/count.hpp:4542:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 4542 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/count.cc:3: In file included from stan_files/count.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 19 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/jm.stan Wrote C++ file "stan_files/jm.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/jm.cc -o stan_files/jm.o In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/jm.cc:3: stan_files/jm.hpp:6340:15: warning: variable 'shift_nb' set but not used [-Wunused-but-set-variable] 6340 | int shift_nb = std::numeric_limits::min(); | ^ stan_files/jm.hpp:6341:15: warning: variable 'shift_lb' set but not used [-Wunused-but-set-variable] 6341 | int shift_lb = std::numeric_limits::min(); | ^ stan_files/jm.hpp:6342:15: warning: variable 'shift_ub' set but not used [-Wunused-but-set-variable] 6342 | int shift_ub = std::numeric_limits::min(); | ^ stan_files/jm.hpp:15492:13: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 15492 | int mark = std::numeric_limits::min(); | ^ stan_files/jm.hpp:18219:13: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 18219 | int mark = std::numeric_limits::min(); | ^ stan_files/jm.hpp:18578:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 18578 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/jm.cc:3: In file included from stan_files/jm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ In file included from stan_files/jm.cc:3: stan_files/jm.hpp:5392:15: warning: unused variable 'log_y' [-Wunused-variable] 5392 | const auto& log_y = stan::math::to_ref(log_y_arg__); | ^~~~~ stan_files/jm.hpp:15658:26: note: in instantiation of function template specialization 'model_jm_namespace::glm_lpdf>, Eigen::Matrix, double, double, Eigen::Map>, Eigen::Map>, nullptr>' requested here 15658 | lp_accum__.add(glm_lpdf(yReal1, yInt1, yEta1, yAux1, | ^ stan_files/jm.hpp:20794:12: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob_impl, std::vector, nullptr, nullptr>' requested here 20794 | return log_prob_impl(params_r, params_i, pstream); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/util/initialize.hpp:129:33: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob' requested here 129 | log_prob = model.template log_prob(unconstrained, | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here 49 | std::vector cont_vector = util::initialize( | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here 481 | return_code = stan::services::diagnose::diagnose(model, | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here 1215 | ret = command(args, model_, holder, names_oi_tidx_, | ^ stan_files/jm.cc:13:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here 13 | .method("call_sampler", &rstan::stan_fit ::call_sampler) | ^ In file included from stan_files/jm.cc:3: stan_files/jm.hpp:5999:15: warning: unused variable 'scale' [-Wunused-variable] 5999 | const auto& scale = stan::math::to_ref(scale_arg__); | ^~~~~ stan_files/jm.hpp:17548:24: note: in instantiation of function template specialization 'model_jm_namespace::basehaz_lpdf, Eigen::Map>, Eigen::Map>, nullptr>' requested here 17548 | lp_accum__.add(basehaz_lpdf(e_aux_unscaled, | ^ stan_files/jm.hpp:20794:12: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob_impl, std::vector, nullptr, nullptr>' requested here 20794 | return log_prob_impl(params_r, params_i, pstream); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/util/initialize.hpp:129:33: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob' requested here 129 | log_prob = model.template log_prob(unconstrained, | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here 49 | std::vector cont_vector = util::initialize( | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here 481 | return_code = stan::services::diagnose::diagnose(model, | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here 1215 | ret = command(args, model_, holder, names_oi_tidx_, | ^ stan_files/jm.cc:13:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here 13 | .method("call_sampler", &rstan::stan_fit ::call_sampler) | ^ In file included from stan_files/jm.cc:3: stan_files/jm.hpp:5392:15: warning: unused variable 'log_y' [-Wunused-variable] 5392 | const auto& log_y = stan::math::to_ref(log_y_arg__); | ^~~~~ stan_files/jm.hpp:15658:26: note: in instantiation of function template specialization 'model_jm_namespace::glm_lpdf>, Eigen::Matrix, -1, 1>, stan::math::var_value, double, Eigen::Map>, Eigen::Map>, nullptr>' requested here 15658 | lp_accum__.add(glm_lpdf(yReal1, yInt1, yEta1, yAux1, | ^ stan_files/jm.hpp:20794:12: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob_impl>, std::vector, nullptr, nullptr>' requested here 20794 | return log_prob_impl(params_r, params_i, pstream); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob>' requested here 40 | var adLogProb = model.template log_prob( | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/util/initialize.hpp:167:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad' requested here 167 | log_prob = stan::model::log_prob_grad( | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here 49 | std::vector cont_vector = util::initialize( | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here 481 | return_code = stan::services::diagnose::diagnose(model, | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here 1215 | ret = command(args, model_, holder, names_oi_tidx_, | ^ stan_files/jm.cc:13:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here 13 | .method("call_sampler", &rstan::stan_fit ::call_sampler) | ^ In file included from stan_files/jm.cc:3: stan_files/jm.hpp:5999:15: warning: unused variable 'scale' [-Wunused-variable] 5999 | const auto& scale = stan::math::to_ref(scale_arg__); | ^~~~~ stan_files/jm.hpp:17548:24: note: in instantiation of function template specialization 'model_jm_namespace::basehaz_lpdf, -1, 1>, Eigen::Map>, Eigen::Map>, nullptr>' requested here 17548 | lp_accum__.add(basehaz_lpdf(e_aux_unscaled, | ^ stan_files/jm.hpp:20794:12: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob_impl>, std::vector, nullptr, nullptr>' requested here 20794 | return log_prob_impl(params_r, params_i, pstream); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_jm_namespace::model_jm::log_prob>' requested here 40 | var adLogProb = model.template log_prob( | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/util/initialize.hpp:167:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad' requested here 167 | log_prob = stan::model::log_prob_grad( | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here 49 | std::vector cont_vector = util::initialize( | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here 481 | return_code = stan::services::diagnose::diagnose(model, | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here 1215 | ret = command(args, model_, holder, names_oi_tidx_, | ^ stan_files/jm.cc:13:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here 13 | .method("call_sampler", &rstan::stan_fit ::call_sampler) | ^ 28 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan Wrote C++ file "stan_files/lm.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/lm.cc -o stan_files/lm.o In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/lm.cc:3: stan_files/lm.hpp:950:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 950 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/lm.cc:3: In file included from stan_files/lm.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 19 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/mvmer.stan Wrote C++ file "stan_files/mvmer.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/mvmer.cc -o stan_files/mvmer.o In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/mvmer.cc:3: stan_files/mvmer.hpp:8870:13: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 8870 | int mark = std::numeric_limits::min(); | ^ stan_files/mvmer.hpp:9784:13: warning: variable 'mark' set but not used [-Wunused-but-set-variable] 9784 | int mark = std::numeric_limits::min(); | ^ stan_files/mvmer.hpp:10107:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 10107 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/mvmer.cc:3: In file included from stan_files/mvmer.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ In file included from stan_files/mvmer.cc:3: stan_files/mvmer.hpp:4495:15: warning: unused variable 'log_y' [-Wunused-variable] 4495 | const auto& log_y = stan::math::to_ref(log_y_arg__); | ^~~~~ stan_files/mvmer.hpp:9019:26: note: in instantiation of function template specialization 'model_mvmer_namespace::glm_lpdf>, Eigen::Matrix, double, double, Eigen::Map>, Eigen::Map>, nullptr>' requested here 9019 | lp_accum__.add(glm_lpdf(yReal1, yInt1, yEta1, yAux1, | ^ stan_files/mvmer.hpp:11772:12: note: in instantiation of function template specialization 'model_mvmer_namespace::model_mvmer::log_prob_impl, std::vector, nullptr, nullptr>' requested here 11772 | return log_prob_impl(params_r, params_i, pstream); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/util/initialize.hpp:129:33: note: in instantiation of function template specialization 'model_mvmer_namespace::model_mvmer::log_prob' requested here 129 | log_prob = model.template log_prob(unconstrained, | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here 49 | std::vector cont_vector = util::initialize( | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here 481 | return_code = stan::services::diagnose::diagnose(model, | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here 1215 | ret = command(args, model_, holder, names_oi_tidx_, | ^ stan_files/mvmer.cc:13:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here 13 | .method("call_sampler", &rstan::stan_fit ::call_sampler) | ^ In file included from stan_files/mvmer.cc:3: stan_files/mvmer.hpp:4495:15: warning: unused variable 'log_y' [-Wunused-variable] 4495 | const auto& log_y = stan::math::to_ref(log_y_arg__); | ^~~~~ stan_files/mvmer.hpp:9019:26: note: in instantiation of function template specialization 'model_mvmer_namespace::glm_lpdf>, Eigen::Matrix, -1, 1>, stan::math::var_value, double, Eigen::Map>, Eigen::Map>, nullptr>' requested here 9019 | lp_accum__.add(glm_lpdf(yReal1, yInt1, yEta1, yAux1, | ^ stan_files/mvmer.hpp:11772:12: note: in instantiation of function template specialization 'model_mvmer_namespace::model_mvmer::log_prob_impl>, std::vector, nullptr, nullptr>' requested here 11772 | return log_prob_impl(params_r, params_i, pstream); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:36: note: in instantiation of function template specialization 'model_mvmer_namespace::model_mvmer::log_prob>' requested here 40 | var adLogProb = model.template log_prob( | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/util/initialize.hpp:167:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad' requested here 167 | log_prob = stan::model::log_prob_grad( | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize, boost::random::linear_congruential_engine>>' requested here 49 | std::vector cont_vector = util::initialize( | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose' requested here 481 | return_code = stan::services::diagnose::diagnose(model, | ^ /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command, boost::random::linear_congruential_engine>>' requested here 1215 | ret = command(args, model_, holder, names_oi_tidx_, | ^ stan_files/mvmer.cc:13:87: note: in instantiation of member function 'rstan::stan_fit, boost::random::linear_congruential_engine>>::call_sampler' requested here 13 | .method("call_sampler", &rstan::stan_fit ::call_sampler) | ^ 23 warnings generated. "/data/gannet/ripley/R/R-clang/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/polr.stan Wrote C++ file "stan_files/polr.cc" /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c stan_files/polr.cc -o stan_files/polr.o In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable] 273 | Index count = 0; | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:3: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35: /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] 78 | Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree | ^ /data/gannet/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable] 79 | Index nsuper_et = 0; // Number of relaxed snodes in the original etree | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 47 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:21: /data/gannet/ripley/R/test-clang/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] 70 | virtual std::streamsize xsputn(const char_type* s, int n) { | ^ /usr/local/clang18/bin/../include/c++/v1/streambuf:276:22: note: hidden overloaded virtual function 'std::basic_streambuf::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') 276 | virtual streamsize xsputn(const char_type* __s, streamsize __n); | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable] 72 | Index replacements = 0; | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:31: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37: In file included from /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /data/gannet/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable] 246 | int count = 0; | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 57 | struct ops_partials_edge> { | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? 45 | class ops_partials_edge; | ^~~~~ | struct In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:34: /data/gannet/ripley/R/test-clang/BH/include/boost/units/static_rational.hpp:166:10: warning: extension used [-Wlanguage-extension-token] 166 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:125:10: warning: extension used [-Wlanguage-extension-token] 125 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:35: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimension.hpp:21: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/dimension_list.hpp:131: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dimensionless_type.hpp:49:10: warning: extension used [-Wlanguage-extension-token] 49 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:39: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/linear_algebra.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/dim.hpp:75:10: warning: extension used [-Wlanguage-extension-token] 75 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:40: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/unscale.hpp:28: /data/gannet/ripley/R/test-clang/BH/include/boost/units/scale.hpp:139:10: warning: extension used [-Wlanguage-extension-token] 139 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:20: /data/gannet/ripley/R/test-clang/BH/include/boost/units/heterogeneous_system.hpp:120:10: warning: extension used [-Wlanguage-extension-token] 120 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:29: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/conversion.hpp:17: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/units/detail/conversion_impl.hpp:21: /data/gannet/ripley/R/test-clang/BH/include/boost/units/homogeneous_system.hpp:99:10: warning: extension used [-Wlanguage-extension-token] 99 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:15: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor.hpp:16: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint.hpp:25: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:30: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/algebra/default_operations.hpp:26: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/numeric/odeint/util/unit_helper.hpp:23: /data/gannet/ripley/R/test-clang/BH/include/boost/units/quantity.hpp:495:10: warning: extension used [-Wlanguage-extension-token] 495 | #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP() | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/typeof/typeof.hpp:28:13: note: expanded from macro 'BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP' 28 | | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: /data/gannet/ripley/R/test-clang/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 stan_files/polr.cc:3: stan_files/polr.hpp:629:9: warning: variable 'iter' set but not used [-Wunused-but-set-variable] 629 | int iter = std::numeric_limits::min(); | ^ stan_files/polr.hpp:1872:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] 1872 | int pos__ = std::numeric_limits::min(); | ^ In file included from stan_files/polr.cc:3: In file included from stan_files/polr.hpp:18: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/rstaninc.hpp:4: In file included from /data/gannet/ripley/R/test-clang/rstan/include/rstan/stan_fit.hpp:43: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim.hpp:14: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/beta.hpp:1721: /data/gannet/ripley/R/test-clang/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); | ^~~~~~~~~ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder::temme_root_finder' requested here 304 | temme_root_finder(-lu, alpha), x, lower, upper, policies::digits() / 2); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 615 | x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp, boost::math::policies::promote_float, boost::math::policies::promote_double>>' requested here 992 | rx = detail::ibeta_inv_imp( | ^ /data/gannet/ripley/R/test-clang/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 1023 | return ibeta_inv(a, b, p, static_cast(nullptr), pol); | ^ /data/gannet/ripley/R/test-clang/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv, boost::math::policies::pole_error, boost::math::policies::promote_double, boost::math::policies::digits2<>>>' requested here 32 | return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); | ^ 20 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-clang/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'/data/gannet/ripley/R/test-clang/StanHeaders/include' -I'/data/gannet/ripley/R/test-clang/rstan/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppEigen/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c init.cpp -o init.o /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rstanarm.so stan_files/bernoulli.o stan_files/binomial.o stan_files/continuous.o stan_files/count.o stan_files/jm.o stan_files/lm.o stan_files/mvmer.o stan_files/polr.o init.o -L/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -Wl,-rpath,/data/gannet/ripley/R/test-clang/RcppParallel/lib/ -ltbb -ltbbmalloc rm stan_files/polr.cc stan_files/mvmer.cc stan_files/count.cc stan_files/lm.cc stan_files/jm.cc stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rstanarm/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rstanarm/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rstanarm/src' installing to /data/gannet/ripley/R/packages/tests-clang/rstanarm.Rcheck/00LOCK-rstanarm/00new/rstanarm/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (rstanarm)