Can not install Rstan in R4.1 on Centos7

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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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::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

Start by reviewing the R 4.1/CentOS 7 installation log, especially the failure reported while compiling stan/lang/ast_def.cpp and the R Makeconf path shown. Reproduce the rstan installation in the stated environment and identify the missing or incompatible build requirement; done means rstan installs successfully there.