Can not install Rstan in R4.1 on Centos7
Open
vicscott
opened this issue 2 years ago
•
12 comments
Summary:
make: *** [/datb/home/wanglab27/bin/r_base/R-4.1.0/etc/Makeconf:177: stan_fit.o] Error 1
ERROR: compilation failed for package ‘rstan’
Description:
** libs
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c chains.cpp -o chains.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c pointer-tools.cpp -o pointer-tools.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan_fit_base.cpp -o stan_fit_base.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stanc.cpp -o stanc.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c Module.cpp -o Module.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan_fit_rccp.cpp -o stan_fit_rccp.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c misc.cpp -o misc.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c sparse_extractors.cpp -o sparse_extractors.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/ast_def.cpp -o stan/lang/ast_def.o
In file included from stan/lang/ast_def.cpp:97:0:
./stan/lang/ast/sigs/function_signatures_def.hpp: In constructor ‘stan::lang::function_signatures::function_signatures()’:
./stan/lang/ast/sigs/function_signatures_def.hpp:474:1: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
function_signatures::function_signatures() {
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/program_grammar_inst.cpp -o stan/lang/grammars/program_grammar_inst.o
In file included from ./stan/lang/grammars/program_grammar_def.hpp:10:0,
from stan/lang/grammars/program_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/expression_grammar_inst.cpp -o stan/lang/grammars/expression_grammar_inst.o
In file included from ./stan/lang/grammars/expression_grammar_def.hpp:6:0,
from stan/lang/grammars/expression_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/statement_grammar_inst.cpp -o stan/lang/grammars/statement_grammar_inst.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/expression07_grammar_inst.cpp -o stan/lang/grammars/expression07_grammar_inst.o
In file included from ./stan/lang/grammars/expression07_grammar_def.hpp:7:0,
from stan/lang/grammars/expression07_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/statement_2_grammar_inst.cpp -o stan/lang/grammars/statement_2_grammar_inst.o
In file included from ./stan/lang/grammars/statement_2_grammar_def.hpp:10:0,
from stan/lang/grammars/statement_2_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/block_var_decls_grammar_inst.cpp -o stan/lang/grammars/block_var_decls_grammar_inst.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/indexes_grammar_inst.cpp -o stan/lang/grammars/indexes_grammar_inst.o
In file included from ./stan/lang/grammars/indexes_grammar_def.hpp:9:0,
from stan/lang/grammars/indexes_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/local_var_decls_grammar_inst.cpp -o stan/lang/grammars/local_var_decls_grammar_inst.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/semantic_actions_def.cpp -o stan/lang/grammars/semantic_actions_def.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/whitespace_grammar_inst.cpp -o stan/lang/grammars/whitespace_grammar_inst.o
In file included from ./stan/lang/grammars/whitespace_grammar_def.hpp:7:0,
from stan/lang/grammars/whitespace_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/bare_type_grammar_inst.cpp -o stan/lang/grammars/bare_type_grammar_inst.o
In file included from ./stan/lang/grammars/bare_type_grammar_def.hpp:8:0,
from stan/lang/grammars/bare_type_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/term_grammar_inst.cpp -o stan/lang/grammars/term_grammar_inst.o
In file included from ./stan/lang/grammars/term_grammar_def.hpp:11:0,
from stan/lang/grammars/term_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan/lang/grammars/functions_grammar_inst.cpp -o stan/lang/grammars/functions_grammar_inst.o
In file included from ./stan/lang/grammars/functions_grammar_def.hpp:9:0,
from stan/lang/grammars/functions_grammar_inst.cpp:1:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
g++ -std=gnu++14 -shared -L/usr/local/lib64 -o rstan.so chains.o pointer-tools.o stan_fit_base.o init.o stanc.o Module.o stan_fit_rccp.o misc.o sparse_extractors.o stan/lang/ast_def.o stan/lang/grammars/program_grammar_inst.o stan/lang/grammars/expression_grammar_inst.o stan/lang/grammars/statement_grammar_inst.o stan/lang/grammars/expression07_grammar_inst.o stan/lang/grammars/statement_2_grammar_inst.o stan/lang/grammars/block_var_decls_grammar_inst.o stan/lang/grammars/indexes_grammar_inst.o stan/lang/grammars/local_var_decls_grammar_inst.o stan/lang/grammars/semantic_actions_def.o stan/lang/grammars/whitespace_grammar_inst.o stan/lang/grammars/bare_type_grammar_inst.o stan/lang/grammars/term_grammar_inst.o stan/lang/grammars/functions_grammar_inst.o
g++ -std=gnu++14 -I"/datb/home/wanglab27/bin/r_base/R-4.1.0/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/Rcpp/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppEigen/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include' -I'/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c stan_fit.cpp -o stan_fit.o
In file included from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:14:0,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat.hpp:142,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp: In instantiation of ‘struct boost::math::tools::integer_scalar_type<double, true>’:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:209:72: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:252:51: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:53: required from here
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp:50:44: error: ‘double’ is not a class, struct, or union type
typedef typename T::value_type type;
^
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp: In instantiation of ‘struct boost::math::tools::scalar_type<double, true>’:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:210:63: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:252:51: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:53: required from here
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp:70:44: error: ‘double’ is not a class, struct, or union type
typedef typename T::value_type type;
^
In file included from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:18:0,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat.hpp:142,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp: In instantiation of ‘struct boost::math::tools::detail::tiny_value<double, true>’:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:214:60: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:252:51: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:53: required from here
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:84:48: error: ‘double’ is not a class, struct, or union type
using value_type = typename T::value_type;
^
In file included from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:14:0,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat.hpp:142,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp: In instantiation of ‘struct boost::math::tools::integer_scalar_type<long double, true>’:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:209:72: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long unsigned int]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:252:51: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_q.hpp:54:77: required from here
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp:50:44: error: ‘long double’ is not a class, struct, or union type
typedef typename T::value_type type;
^
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp: In instantiation of ‘struct boost::math::tools::scalar_type<long double, true>’:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:210:63: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long unsigned int]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:252:51: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_q.hpp:54:77: required from here
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/complex.hpp:70:44: error: ‘long double’ is not a class, struct, or union type
typedef typename T::value_type type;
^
In file included from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:18:0,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/mat.hpp:142,
from /newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp: In instantiation of ‘struct boost::math::tools::detail::tiny_value<long double, true>’:
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:214:60: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long unsigned int]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:252:51: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/StanHeaders/include/stan/math/prim/scal/fun/gamma_q.hpp:54:77: required from here
/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/BH/include/boost/math/tools/fraction.hpp:84:48: error: ‘long double’ is not a class, struct, or union type
using value_type = typename T::value_type;
^
make: *** [/datb/home/wanglab27/bin/r_base/R-4.1.0/etc/Makeconf:177: stan_fit.o] Error 1
ERROR: compilation failed for package ‘rstan’
removing ‘/newdatc/home/wanglab27/bin/r_base/R-4.1.0/library/rstan’
The downloaded source packages are in
‘/tmp/RtmpgGnu0X/downloaded_packages’
Warning message:
In install.packages("rstan") :
installation of package ‘rstan’ had non-zero exit status
R Version:
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /newdatc/home/wanglab27/bin/r_base/R-4.1.0/lib/libRblas.so
LAPACK: /newdatc/home/wanglab27/bin/r_base/R-4.1.0/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0
Operating System:
Centos7
any help is appreciated!!!
What version of g++ do you have installed?
What version of g++ do you have installed?
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/newdatc/home/wanglab27/bin/gcc49/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --disable-multilib --enable-languages=c,c++ --prefix=/newdatc/home/wanglab27/bin/gcc49/
Thread model: posix
gcc version 4.9.2 (GCC)
Well, I think my gcc tool chain is OK
Hello,
I have the same issue. Were you able to solve this?
thanks.
It has been a long time for this and I can not recall clearly.
I tried conda install it but I am not sure whether it worked.
---Original---
From: @ >
Date: Wed, Jun 1, 2022 18:26 PM
To: @ @ @
Hello,
I have the same issue. Were you able to solve this?
thanks.
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: @
@andrjohns
Any updates on the issue?
it also happened to R 3.6 in windows by running the following
remove.packages("rstan")
if (file.exists(".RData")) file.remove(".RData")
#Restart R Session
#Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1) # only necessary for Linux without the nodejs library / headers
install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)
PS : gcc tool chain is working also
@cse387 Can you clarify what your issue is? You're installing rstan on windows in R3.6 and receiving the error:
...library/BH/include/boost/math/tools/complex.hpp:50:44: error: ‘double’ is not a class, struct, or union type
typedef typename T::value_type type;
Is that right? Or are you receiving a different error?
@andrjohns Hello Adrew thanks for the prompt reply
Exactly this is the error just for the discussion economy,
I have configured the following according to variety of direction from other posts/comments
Roots 3.5 (with path settings option)
readLines("~/.Renviron")
"PATH="C:/Rtools/bin;${PATH}""
readLines("~/.Rprofile")
"Sys.setenv(BINPREF = "C:/Rtools/mingw_$(WIN)/bin/")"
readLines("~/.R/Makevars.win")
"CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function"
"CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y"
"CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function"
The architecture of my machine is x64 bit!
Thanks
Can you post the R command that you're running and the full error output that's being returned?
Yes sure here it's the code snippet I run according to https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
remove.packages("rstan")
if (file.exists(".RData")) file.remove(".RData")
#Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1) # only necessary for Linux without the nodejs library / headers
install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)#
Installing package into ‘C:/Users/john/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rstan 2.21.2 2.21.5 TRUE
installing the source package ‘rstan’
trying URL 'https://cloud.r-project.org/src/contrib/rstan_2.21.5.tar.gz'
Content type 'application/x-gzip' length 1189130 bytes (1.1 MB)
downloaded 1.1 MB
installing source package 'rstan' ...
** package 'rstan' successfully unpacked and MD5 sums checked
** using staged installation
** libs
*** arch - i386
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c sparse_extractors.cpp -o sparse_extractors.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c misc.cpp -o misc.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan_fit_rccp.cpp -o stan_fit_rccp.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c Module.cpp -o Module.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stanc.cpp -o stanc.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan_fit_base.cpp -o stan_fit_base.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c pointer-tools.cpp -o pointer-tools.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c chains.cpp -o chains.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/ast_def.cpp -o stan/lang/ast_def.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/functions_grammar_inst.cpp -o stan/lang/grammars/functions_grammar_inst.o
In file included from ./stan/lang/grammars/functions_grammar_def.hpp:9:0,
from stan/lang/grammars/functions_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/term_grammar_inst.cpp -o stan/lang/grammars/term_grammar_inst.o
In file included from ./stan/lang/grammars/term_grammar_def.hpp:11:0,
from stan/lang/grammars/term_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/bare_type_grammar_inst.cpp -o stan/lang/grammars/bare_type_grammar_inst.o
In file included from ./stan/lang/grammars/bare_type_grammar_def.hpp:8:0,
from stan/lang/grammars/bare_type_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/whitespace_grammar_inst.cpp -o stan/lang/grammars/whitespace_grammar_inst.o
In file included from ./stan/lang/grammars/whitespace_grammar_def.hpp:7:0,
from stan/lang/grammars/whitespace_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/semantic_actions_def.cpp -o stan/lang/grammars/semantic_actions_def.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/local_var_decls_grammar_inst.cpp -o stan/lang/grammars/local_var_decls_grammar_inst.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/indexes_grammar_inst.cpp -o stan/lang/grammars/indexes_grammar_inst.o
In file included from ./stan/lang/grammars/indexes_grammar_def.hpp:9:0,
from stan/lang/grammars/indexes_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/block_var_decls_grammar_inst.cpp -o stan/lang/grammars/block_var_decls_grammar_inst.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/statement_2_grammar_inst.cpp -o stan/lang/grammars/statement_2_grammar_inst.o
In file included from ./stan/lang/grammars/statement_2_grammar_def.hpp:10:0,
from stan/lang/grammars/statement_2_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/expression07_grammar_inst.cpp -o stan/lang/grammars/expression07_grammar_inst.o
In file included from ./stan/lang/grammars/expression07_grammar_def.hpp:7:0,
from stan/lang/grammars/expression07_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/statement_grammar_inst.cpp -o stan/lang/grammars/statement_grammar_inst.o
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/expression_grammar_inst.cpp -o stan/lang/grammars/expression_grammar_inst.o
In file included from ./stan/lang/grammars/expression_grammar_def.hpp:6:0,
from stan/lang/grammars/expression_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan/lang/grammars/program_grammar_inst.cpp -o stan/lang/grammars/program_grammar_inst.o
In file included from ./stan/lang/grammars/program_grammar_def.hpp:10:0,
from stan/lang/grammars/program_grammar_inst.cpp:1:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/spirit/include/phoenix_core.hpp:12:81: note: #pragma message: This header is deprecated. Use <boost/phoenix/core.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/phoenix/core.hpp>")
^
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -shared -s -static-libgcc -o rstan.dll tmp.def sparse_extractors.o misc.o stan_fit_rccp.o Module.o stanc.o init.o stan_fit_base.o pointer-tools.o chains.o stan/lang/ast_def.o stan/lang/grammars/functions_grammar_inst.o stan/lang/grammars/term_grammar_inst.o stan/lang/grammars/bare_type_grammar_inst.o stan/lang/grammars/whitespace_grammar_inst.o stan/lang/grammars/semantic_actions_def.o stan/lang/grammars/local_var_decls_grammar_inst.o stan/lang/grammars/indexes_grammar_inst.o stan/lang/grammars/block_var_decls_grammar_inst.o stan/lang/grammars/statement_2_grammar_inst.o stan/lang/grammars/expression07_grammar_inst.o stan/lang/grammars/statement_grammar_inst.o stan/lang/grammars/expression_grammar_inst.o stan/lang/grammars/program_grammar_inst.o -LC:/Users/john/Documents/R/win-library/3.6/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/PROGRA~1/R/R-36~1.2/bin/i386 -lR
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -DSTAN_THREADS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -O3 -Wno-unused-variable -Wno-unused-function -c stan_fit.cpp -o stan_fit.o
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:14:0,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:142,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::integer_scalar_type<double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:209:72: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:53: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:50:44: error: 'double' is not a class, struct, or union type
typedef typename T::value_type type;
^
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::scalar_type<double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:210:63: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:53: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:70:44: error: 'double' is not a class, struct, or union type
typedef typename T::value_type type;
^
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18:0,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:142,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp: In instantiation of 'struct boost::math::tools::detail::tiny_value<double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:214:60: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double >; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/gamma_p.hpp:76:53: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:84:48: error: 'double' is not a class, struct, or union type
using value_type = typename T::value_type;
^
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:14:0,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:142,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::integer_scalar_type<long double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:209:72: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/gamma_q.hpp:54:77: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:50:44: error: 'long double' is not a class, struct, or union type
typedef typename T::value_type type;
^
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::scalar_type<long double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:210:63: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/gamma_q.hpp:54:77: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:70:44: error: 'long double' is not a class, struct, or union type
typedef typename T::value_type type;
^
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18:0,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/lgamma.hpp:44,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/lgamma.hpp:5,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:142,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
from ./stan/model/log_prob_grad.hpp:4,
from ./stan/model/test_gradients.hpp:7,
from ./stan/services/diagnose/diagnose.hpp:10,
from stan_fit.cpp:33:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp: In instantiation of 'struct boost::math::tools::detail::tiny_value<long double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:214:60: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from 'typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/scal/fun/gamma_q.hpp:54:77: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:84:48: error: 'long double' is not a class, struct, or union type
using value_type = typename T::value_type;
^
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/i386/Makeconf:215: stan_fit.o] Error 1
ERROR: compilation failed for package 'rstan'
removing 'C:/Users/john/Documents/R/win-library/3.6/rstan'
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\john\AppData\Local\Temp\RtmpotQixI\downloaded_packages’
Can I get you to try the preview of the next RStan version to see if the problem still exists:
remove.packages(c("StanHeaders", "rstan"))
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
hello thanks for ur assistance
the Stanheaders has been successfully installed, although not the rstan package
here is the output
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
Installing package into ‘C:/Users/john/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rstan 2.21.2 2.26.11 TRUE
installing the source package ‘rstan’
trying URL 'https://mc-stan.org/r-packages/src/contrib/rstan_2.26.11.tar.gz'
Content type 'application/gzip' length 1041484 bytes (1017 KB)
downloaded 1017 KB
installing source package 'rstan' ...
** using staged installation
** libs
*** arch - i386
C:/Rtools/mingw_32/bin/g++ -m32 -std=c++1y -I"C:/PROGRA~1/R/R-36~1.2/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -DBOOST_NO_AUTO_PTR -D_REENTRANT -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/john/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppEigen/include" -I"C:/Users/john/Documents/R/win-library/3.6/BH/include" -I"C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include" -I"C:/Users/john/Documents/R/win-library/3.6/RcppParallel/include" -DRCPP_PARALLEL_USE_TBB=1 -DSTRICT_R_HEADERS -O3 -Wno-unused-variable -Wno-unused-function -c sparse_extractors.cpp -o sparse_extractors.o
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:14:0,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/bessel.hpp:20,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun.hpp:28,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim.hpp:14,
from sparse_extractors.cpp:2:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::integer_scalar_type<double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:209:72: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:50:44: error: 'double' is not a class, struct, or union type
typedef typename T::value_type type;
^
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::scalar_type<double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:210:63: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:70:44: error: 'double' is not a class, struct, or union type
typedef typename T::value_type type;
^
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18:0,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/bessel.hpp:20,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun.hpp:28,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim.hpp:14,
from sparse_extractors.cpp:2:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp: In instantiation of 'struct boost::math::tools::detail::tiny_value<double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:214:60: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2125:55: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::pole_error<(boost::math::policies::error_policy_type)1u>, boost::math::policies::promote_double, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:84:48: error: 'double' is not a class, struct, or union type
using value_type = typename T::value_type;
^
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:14:0,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/bessel.hpp:20,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun.hpp:28,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim.hpp:14,
from sparse_extractors.cpp:2:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::integer_scalar_type<long double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:209:72: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/gamma_q.hpp:55:77: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:50:44: error: 'long double' is not a class, struct, or union type
typedef typename T::value_type type;
^
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp: In instantiation of 'struct boost::math::tools::scalar_type<long double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:210:63: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/gamma_q.hpp:55:77: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/complex.hpp:70:44: error: 'long double' is not a class, struct, or union type
typedef typename T::value_type type;
^
In file included from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:18:0,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/bessel.hpp:20,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun.hpp:28,
from C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim.hpp:14,
from sparse_extractors.cpp:2:
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp: In instantiation of 'struct boost::math::tools::detail::tiny_value<long double, true>':
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:214:60: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double; uintmax_t = long long unsigned int]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:252:51: required from 'typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:313:75: required from 'T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = long double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:1175:85: required from 'T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::promote_float, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2094:55: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_q(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/special_functions/gamma.hpp:2100:45: required from 'typename boost::math::tools::promote_args<T1, T2>::type boost::math::gamma_q(RT1, RT2) [with RT1 = double; RT2 = double; typename boost::math::tools::promote_args<T1, T2>::type = double]'
C:/Users/john/Documents/R/win-library/3.6/StanHeaders/include/stan/math/prim/fun/gamma_q.hpp:55:77: required from here
C:/Users/john/Documents/R/win-library/3.6/BH/include/boost/math/tools/fraction.hpp:84:48: error: 'long double' is not a class, struct, or union type
using value_type = typename T::value_type;
^
make: *** [C:/PROGRA~1/R/R-36~1.2/etc/i386/Makeconf:215: sparse_extractors.o] Error 1
ERROR: compilation failed for package 'rstan'
removing 'C:/Users/john/Documents/R/win-library/3.6/rstan'
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\john\AppData\Local\Temp\Rtmpy8s6Y1\downloaded_packages’
rstan copied to clipboard
stan-dev
