* using log directory 'd:/Rcompile/CRANpkg/local/3.5/rstap.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'rstap/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rstap' version '1.0.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'rstap' can be installed ... ERROR Installation failed. See 'd:/Rcompile/CRANpkg/local/3.5/rstap.Rcheck/00install.out' for details. * DONE The installation logfile: * installing *source* package 'rstap' ... ** package 'rstap' successfully unpacked and MD5 sums checked ** libs *** arch - i386 make[1]: Entering directory `/cygdrive/d/temp/RtmpCs69Kn/R.INSTALL2798656c16bb/rstap/src-i386' "D:/RCompile/recent/R-3.5.3/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/stap_bernoulli.stan Wrote C++ file "stan_files/stap_bernoulli.cc" d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -std=gnu++14 -I"D:/RCompile/recent/R-3.5.3/include" -DNDEBUG -I"../inst/include" -I"d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I"d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include" -I"d:/RCompile/CRANpkg/lib/3.5/rstan/include" -I"d:/RCompile/CRANpkg/lib/3.5/BH/include" -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.5/RcppEigen/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c stan_files/stap_bernoulli.cc -o stan_files/stap_bernoulli.o In file included from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat.hpp:336, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/mat.hpp:12, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/stan_fit.hpp:35, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/rstaninc.hpp:3, from stan_files/stap_bernoulli.hpp:18, from stan_files/stap_bernoulli.cc:3: d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function 'typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)': d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef 'T_alpha_val' locally defined but not used [-Wunused-local-typedefs] typename partials_return_type::type>::type T_alpha_val; ^ In file included from stan_files/stap_bernoulli.cc:3:0: stan_files/stap_bernoulli.hpp: In function 'void model_stap_bernoulli_namespace::decov_lp(const Eigen::Matrix&, const Eigen::Matrix&, const Eigen::Matrix&, const Eigen::Matrix&, const Eigen::Matrix&, const std::vector&, const std::vector&, const Eigen::Matrix&, const int&, const std::vector&, T_lp__&, T_lp_accum__&, std::ostream*)': stan_files/stap_bernoulli.hpp:611:30: warning: typedef 'fun_return_scalar_t__' locally defined but not used [-Wunused-local-typedefs] typedef local_scalar_t__ fun_return_scalar_t__; ^ In file included from stan_files/stap_bernoulli.cc:3:0: stan_files/stap_bernoulli.hpp: In member function 'void model_stap_bernoulli_namespace::model_stap_bernoulli::transform_inits(const stan::io::var_context&, std::vector&, std::vector&, std::ostream*) const': stan_files/stap_bernoulli.hpp:2969:24: warning: typedef 'local_scalar_t__' locally defined but not used [-Wunused-local-typedefs] typedef double local_scalar_t__; ^ In file included from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/core.hpp:45:0, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/mat.hpp:4, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/stan_fit.hpp:35, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/rstaninc.hpp:3, from stan_files/stap_bernoulli.hpp:18, from stan_files/stap_bernoulli.cc:3: d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope: d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function] static void set_zero_all_adjoints() { ^ "D:/RCompile/recent/R-3.5.3/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/stap_binomial.stan Wrote C++ file "stan_files/stap_binomial.cc" d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -std=gnu++14 -I"D:/RCompile/recent/R-3.5.3/include" -DNDEBUG -I"../inst/include" -I"d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I"d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include" -I"d:/RCompile/CRANpkg/lib/3.5/rstan/include" -I"d:/RCompile/CRANpkg/lib/3.5/BH/include" -I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include" -I"d:/RCompile/CRANpkg/lib/3.5/RcppEigen/include" -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2 -c stan_files/stap_binomial.cc -o stan_files/stap_binomial.o In file included from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:0, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat.hpp:336, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/mat.hpp:12, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/stan_fit.hpp:35, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/rstaninc.hpp:3, from stan_files/stap_binomial.hpp:18, from stan_files/stap_binomial.cc:3: d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp: In function 'typename stan::return_type::type stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)': d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: typedef 'T_alpha_val' locally defined but not used [-Wunused-local-typedefs] typename partials_return_type::type>::type T_alpha_val; ^ In file included from stan_files/stap_binomial.cc:3:0: stan_files/stap_binomial.hpp: In function 'void model_stap_binomial_namespace::decov_lp(const Eigen::Matrix&, const Eigen::Matrix&, const Eigen::Matrix&, const Eigen::Matrix&, const Eigen::Matrix&, const std::vector&, const std::vector&, const Eigen::Matrix&, const int&, const std::vector&, T_lp__&, T_lp_accum__&, std::ostream*)': stan_files/stap_binomial.hpp:639:30: warning: typedef 'fun_return_scalar_t__' locally defined but not used [-Wunused-local-typedefs] typedef local_scalar_t__ fun_return_scalar_t__; ^ In file included from stan_files/stap_binomial.cc:3:0: stan_files/stap_binomial.hpp: In member function 'void model_stap_binomial_namespace::model_stap_binomial::transform_inits(const stan::io::var_context&, std::vector&, std::vector&, std::ostream*) const': stan_files/stap_binomial.hpp:2709:24: warning: typedef 'local_scalar_t__' locally defined but not used [-Wunused-local-typedefs] typedef double local_scalar_t__; ^ In file included from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/core.hpp:45:0, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/mat.hpp:4, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/model/test_gradients.hpp:7, from d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/stan_fit.hpp:35, from d:/RCompile/CRANpkg/lib/3.5/rstan/include/rstan/rstaninc.hpp:3, from stan_files/stap_binomial.hpp:18, from stan_files/stap_binomial.cc:3: d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope: d:/RCompile/CRANpkg/lib/3.5/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function] static void set_zero_all_adjoints() { ^ "D:/RCompile/recent/R-3.5.3/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/stap_continuous.stan could not find include file in the following directories: stan_files D:/temp/RtmpCs69Kn/R.INSTALL2798656c16bb/rstap/src-i386 Error in rstan::stanc(file, allow_undefined = TRUE, obfuscate_model_name = FALSE) : failed to parse Stan model 'stap_continuous' due to the above error. Calls: make_cc -> Execution halted make[1]: *** [stan_files/stap_continuous.cc] Error 1 rm stan_files/stap_binomial.cc stan_files/stap_bernoulli.cc make[1]: Leaving directory `/cygdrive/d/temp/RtmpCs69Kn/R.INSTALL2798656c16bb/rstap/src-i386' ERROR: compilation failed for package 'rstap' * removing 'd:/Rcompile/CRANpkg/lib/3.5/rstap' * restoring previous 'd:/Rcompile/CRANpkg/lib/3.5/rstap' In R CMD INSTALL