* installing *source* package ‘CausalQueries’ ...
** this is package ‘CausalQueries’ version ‘1.4.4’
** package ‘CausalQueries’ successfully unpacked and MD5 sums checked
** using staged installation
Registered S3 methods overwritten by 'RcppEigen':
method from
predict.fastLm RcppArmadillo
print.fastLm RcppArmadillo
summary.fastLm RcppArmadillo
print.summary.fastLm RcppArmadillo
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/CausalQueries/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-dev/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-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rstan/include' -I'/data/gannet/ripley/R/test-dev/StanHeaders/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-dev/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-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rstan/include' -I'/data/gannet/ripley/R/test-dev/StanHeaders/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c get_type_prob_helpers_arma.cpp -o get_type_prob_helpers_arma.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-dev/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-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rstan/include' -I'/data/gannet/ripley/R/test-dev/StanHeaders/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c realise_outcome_c.cpp -o realise_outcome_c.o
realise_outcome_c.cpp: In function ‘std::vector<std::vector<std::__cxx11::basic_string<char> > > realise_outcomes_c(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, const std::vector<std::vector<int> >&, const std::vector<int>&, const int&)’:
realise_outcome_c.cpp:52:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
52 | for(int i = 0; i < endogenous_vars.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~
realise_outcome_c.cpp:59:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
59 | for(int k = 0; k < parents_list[endog_var].size(); ++k){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"../inst/include" -I"/data/gannet/ripley/R/test-dev/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-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/rstan/include' -I'/data/gannet/ripley/R/test-dev/StanHeaders/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c stanExports_simplexes.cc -o stanExports_simplexes.o
In file included from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor.hpp:13,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim.hpp:15,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/dump.hpp:7,
from /data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:43,
from /data/gannet/ripley/R/test-dev/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_simplexes.h:23,
from stanExports_simplexes.cc:5:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector<int>&, const int&, const int&, const int&)’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
73 | for (std::size_t i = 0; i < p - 1; i++) {
| ~~^~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
79 | } while (k < x);
| ~~^~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
102 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
105 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector<bool>&, const int&, const double&, const std::vector<int>&, std::vector<double>&)’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
126 | for (std::size_t j = 0; j != k; j++) {
| ~~^~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
132 | while ((first_zero < index.size()) && index[first_zero]) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
135 | if (first_zero == index.size()) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
143 | for (std::size_t i = 0; i != first_zero + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
168 | for (std::size_t i = 1; i != choose_dimk + 1; i++) {
| ~~^~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::dump::vals_c(const std::string&) const’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
694 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
707 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:49:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::random_var_context::vals_c(const std::string&) const’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
111 | for (comp_iter = 0, real_iter = 0; real_iter < val_r.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:68:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::array_var_context::vals_c(const std::string&) const’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
304 | for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
317 | real_iter < val_i->second.first.size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_header.hpp:11,
from stanExports_simplexes.h:25:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp: At global scope:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp:96:20: warning: ‘stan::math::var stan::model::model_base_crtp<M>::log_prob(Eigen::Matrix<stan::math::var_value<double>, -1, 1>&, std::ostream*) const [with M = model_simplexes_namespace::model_simplexes; stan::math::var = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
96 | inline math::var log_prob(Eigen::Matrix<math::var, -1, 1>& theta,
| ^~~~~~~~
stanExports_simplexes.h:1225:3: note: by ‘T_ model_simplexes_namespace::model_simplexes::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
1225 | log_prob(Eigen::Matrix<T_,-1,1>& params_r, std::ostream* pstream = nullptr) const {
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp:154:17: warning: ‘double stan::model::model_base_crtp<M>::log_prob(std::vector<double>&, std::vector<int>&, std::ostream*) const [with M = model_simplexes_namespace::model_simplexes; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
154 | inline double log_prob(std::vector<double>& theta, std::vector<int>& theta_i,
| ^~~~~~~~
stanExports_simplexes.h:1225:3: note: by ‘T_ model_simplexes_namespace::model_simplexes::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
1225 | log_prob(Eigen::Matrix<T_,-1,1>& params_r, std::ostream* pstream = nullptr) const {
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp:91:17: warning: ‘double stan::model::model_base_crtp<M>::log_prob(Eigen::VectorXd&, std::ostream*) const [with M = model_simplexes_namespace::model_simplexes; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
91 | inline double log_prob(Eigen::VectorXd& theta,
| ^~~~~~~~
stanExports_simplexes.h:1225:3: note: by ‘T_ model_simplexes_namespace::model_simplexes::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
1225 | log_prob(Eigen::Matrix<T_,-1,1>& params_r, std::ostream* pstream = nullptr) const {
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp:159:20: warning: ‘stan::math::var stan::model::model_base_crtp<M>::log_prob(std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >&, std::vector<int>&, std::ostream*) const [with M = model_simplexes_namespace::model_simplexes; stan::math::var = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
159 | inline math::var log_prob(std::vector<math::var>& theta,
| ^~~~~~~~
stanExports_simplexes.h:1225:3: note: by ‘T_ model_simplexes_namespace::model_simplexes::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
1225 | log_prob(Eigen::Matrix<T_,-1,1>& params_r, std::ostream* pstream = nullptr) const {
| ^~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp:205:8: warning: ‘void stan::model::model_base_crtp<M>::write_array(boost::random::ecuyer1988&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with M = model_simplexes_namespace::model_simplexes; boost::random::ecuyer1988 = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
205 | void write_array(boost::ecuyer1988& rng, std::vector<double>& theta,
| ^~~~~~~~~~~
stanExports_simplexes.h:1190:3: note: by ‘void model_simplexes_namespace::model_simplexes::write_array(RNG&, Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&, bool, bool, std::ostream*) const’
1190 | write_array(RNG& base_rng, Eigen::Matrix<double,-1,1>& params_r,
| ^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/model_base_crtp.hpp:136:8: warning: ‘void stan::model::model_base_crtp<M>::write_array(boost::random::ecuyer1988&, Eigen::VectorXd&, Eigen::VectorXd&, bool, bool, std::ostream*) const [with M = model_simplexes_namespace::model_simplexes; boost::random::ecuyer1988 = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
136 | void write_array(boost::ecuyer1988& rng, Eigen::VectorXd& theta,
| ^~~~~~~~~~~
stanExports_simplexes.h:1190:3: note: by ‘void model_simplexes_namespace::model_simplexes::write_array(RNG&, Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&, bool, bool, std::ostream*) const’
1190 | write_array(RNG& base_rng, Eigen::Matrix<double,-1,1>& params_r,
| ^~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48: required from here
97 | std::vector<size_t> dim_vec = validate_dims(names, values.size(), dims);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
118 | std::vector<size_t> dim_vec = validate_dims(names, values.size(), dims);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
stanExports_simplexes.h: In instantiation of ‘void model_simplexes_namespace::model_simplexes::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_simplexes.h:1258:27: required from here
1258 | unconstrain_array_impl(params_constrained, params_i,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1259 | params_unconstrained, pstream);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stanExports_simplexes.h:1023:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
1023 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
stanExports_simplexes.h: In instantiation of ‘void model_simplexes_namespace::model_simplexes::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix<double, -1, 1>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_simplexes.h:1268:27: required from here
1268 | unconstrain_array_impl(params_constrained, params_i,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1269 | params_unconstrained, pstream);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stanExports_simplexes.h:1023:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
1023 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
/data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_simplexes_namespace::model_simplexes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_simplexes.cc:30:81: required from here
30 | .method("standalone_gqs", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::standalone_gqs)
| ^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/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 /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err.hpp:4,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim.hpp:12:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan<Eigen::Matrix<double, -1, 1> >(const char*, const char*, const Eigen::Matrix<double, -1, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29 | "not nan");
| ~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:30: required from here
47 | stan::math::check_not_nan(function, "Mean vector", mu);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan<Eigen::Matrix<double, -1, -1> >(const char*, const char*, const Eigen::Matrix<double, -1, -1>&)::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit))))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’
28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29 | "not nan");
| ~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:30: required from here
74 | stan::math::check_not_nan(function, "Cholesky factor", L_chol);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
207 | for (size_t i = 0; i < x.rows(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
208 | for (size_t j = 0; j < x.cols(); j++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_finite<Eigen::Matrix<double, -1, 1> >(const char*, const char*, const Eigen::Matrix<double, -1, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
29 | elementwise_check([](double x) { return std::isfinite(x); }, function, name,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 | y, "finite");
| ~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:29: required from here
21 | stan::math::check_finite("check_finite", "inv_metric", inv_metric);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_positive<Eigen::Matrix<double, -1, 1> >(const char*, const char*, const Eigen::Matrix<double, -1, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
29 | elementwise_check([](double x) { return x > 0; }, function, name, y,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 | "positive");
| ~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:31: required from here
22 | stan::math::check_positive("check_positive", "inv_metric", inv_metric);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/meta.hpp:70,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/core.hpp:4,
from /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim.hpp:10:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t<U, V>* <anonymous> = 0; Idxs = {}]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
79 | stan::math::check_less_or_equal("validate_dims", "array_var_context",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
80 | elem_dims_total[dims.size()], array_size);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
118 | std::vector<size_t> dim_vec = validate_dims(names, values.size(), dims);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare]
39 | if (unlikely(!(y <= high))) {
| ~~~^~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’
9 | #define unlikely(x) __builtin_expect(!!(x), 0)
| ^
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const Eigen::MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_simplexes_namespace::model_simplexes; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_simplexes_namespace::model_simplexes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
1253 | ret = stan::services::standalone_generate(model_, draws,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
1254 | Rcpp::as<unsigned int>(seed), interrupt, logger, *sample_writer_ptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stanExports_simplexes.cc:30:81: required from here
30 | .method("standalone_gqs", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::standalone_gqs)
| ^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
55 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
71 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_finite<Eigen::Matrix<double, 2, 1> >(const char*, const char*, const Eigen::Matrix<double, 2, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, 2, 1>]’
29 | elementwise_check([](double x) { return std::isfinite(x); }, function, name,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 | y, "finite");
| ~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
35 | check_finite("hypergeometric_pFq", "a", a_ref);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
189 | return hypergeometric_pFq(a_args, b_args, z);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
306 | return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
307 | precision, max_steps);
| ~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here
37 | = grad_2F1<true>(a + b, 1.0, a + 1, z);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_finite<Eigen::Matrix<double, 1, 1, 0, 1, 1> >(const char*, const char*, const Eigen::Matrix<double, 1, 1, 0, 1, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, 1, 1, 0, 1, 1>]’
29 | elementwise_check([](double x) { return std::isfinite(x); }, function, name,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 | y, "finite");
| ~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
36 | check_finite("hypergeometric_pFq", "b", b_ref);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
189 | return hypergeometric_pFq(a_args, b_args, z);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
306 | return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
307 | precision, max_steps);
| ~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here
37 | = grad_2F1<true>(a + b, 1.0, a + 1, z);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan<Eigen::Matrix<double, 2, 1> >(const char*, const char*, const Eigen::Matrix<double, 2, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, 2, 1>]’
28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29 | "not nan");
| ~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
39 | check_not_nan("hypergeometric_pFq", "a", a_ref);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
189 | return hypergeometric_pFq(a_args, b_args, z);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
306 | return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
307 | precision, max_steps);
| ~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here
37 | = grad_2F1<true>(a + b, 1.0, a + 1, z);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_not_nan<Eigen::Matrix<double, 1, 1, 0, 1, 1> >(const char*, const char*, const Eigen::Matrix<double, 1, 1, 0, 1, 1>&)::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, 1, 1, 0, 1, 1>]’
28 | elementwise_check([](double x) { return !std::isnan(x); }, function, name, y,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
29 | "not nan");
| ~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16: required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
40 | check_not_nan("hypergeometric_pFq", "b", b_ref);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30: required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
189 | return hypergeometric_pFq(a_args, b_args, z);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39: required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
190 | auto hyper1 = hypergeometric_2F1(a1_euler, a2_euler, b1, z_euler);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57: required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
306 | return internal::grad_2F1_impl<true, true, true, true>(a1, a2, b1, z,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
307 | precision, max_steps);
| ~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:25: required from here
37 | = grad_2F1<true>(a + b, 1.0, a + 1, z);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = check_positive<Eigen::VectorBlock<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, -1> >(const char*, const char*, const Eigen::VectorBlock<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, -1>&)::<lambda(double)>; T = Eigen::VectorBlock<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, -1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((bool)((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime))>* <anonymous> = 0]’:
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::VectorBlock<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, -1>]’
29 | elementwise_check([](double x) { return x > 0; }, function, name, y,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 | "positive");
| ~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:77:19: required from ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&) [with bool propto = false; T_prob = Eigen::VectorBlock<Eigen::Matrix<var_value<double>, -1, 1>, -1>; T_prior_size = Eigen::VectorBlock<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, -1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_prob>* <anonymous> = 0; stan::return_type_t<T1, T2> = var_value<double>]’
77 | check_positive(function, "prior sample sizes", alpha_vec[t]);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stanExports_simplexes.h:735:59: required from ‘stan::scalar_type_t<T2> model_simplexes_namespace::model_simplexes::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
735 | lp_accum__.add(stan::math::dirichlet_lpdf<false>(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
736 | stan::model::rvalue(lambdas, "lambdas",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
737 | stan::model::index_min_max(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
738 | stan::model::rvalue(l_starts, "l_starts",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
739 | stan::model::index_uni(i)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
740 | stan::model::rvalue(l_ends, "l_ends",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
741 | stan::model::index_uni(i)))),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
742 | stan::model::rvalue(lambdas_prior,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
743 | "lambdas_prior",
| ~~~~~~~~~~~~~~~~
744 | stan::model::index_min_max(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
745 | stan::model::rvalue(l_starts, "l_starts",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | stan::model::index_uni(i)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | stan::model::rvalue(l_ends, "l_ends",
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | stan::model::index_uni(i))))));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stanExports_simplexes.h:1232:47: required from ‘T_ model_simplexes_namespace::model_simplexes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
1232 | return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_simplexes_namespace::model_simplexes; std::ostream = std::basic_ostream<char>]’
40 | var adLogProb = model.template log_prob<propto, jacobian_adjust_transform>(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
41 | ad_params_r, params_i, msgs);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_simplexes_namespace::model_simplexes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
1183 | lp = stan::model::log_prob_grad<true,true>(model_, par_r, par_i, gradient, &rstan::io::rcout);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
stanExports_simplexes.cc:23:80: required from here
23 | .method("grad_log_prob", &rstan::stan_fit<stan_model, boost::ecuyer1988> ::grad_log_prob)
| ^~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Block<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, -1, 1, false> >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o CausalQueries.so RcppExports.o get_type_prob_helpers_arma.o realise_outcome_c.o stanExports_simplexes.o -L/data/gannet/ripley/R/test-dev/RcppParallel/lib/ -Wl,-rpath,/data/gannet/ripley/R/test-dev/RcppParallel/lib/ -ltbb -ltbbmalloc
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/CausalQueries/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/CausalQueries/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/CausalQueries/src'
installing to /data/gannet/ripley/R/packages/tests-devel/CausalQueries.Rcheck/00LOCK-CausalQueries/00new/CausalQueries/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CausalQueries)