doing install.packages(“rstan”) on R
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
on a Debian box with recent packages, esp. using:
g++:
Installed: 4:9.2.1-3.1
Candidate: 4:9.2.1-3.1
Version table:
4:10-1 102
102 http://httpredir.debian.org/debian experimental/main amd64 Packages
*** 4:9.2.1-3.1 750
750 http://httpredir.debian.org/debian testing/main amd64 Packages
500 http://httpredir.debian.org/debian unstable/main amd64 Packages
100 /var/lib/dpkg/status
Installation aborts with:
Detailed error message from g++...
n file included from stan/lang/ast_def.cpp:97:
./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
474 | function_signatures::function_signatures() {
| ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/program_grammar_inst.cpp -o stan/lang/grammars/program_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/expression_grammar_inst.cpp -o stan/lang/grammars/expression_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/statement_grammar_inst.cpp -o stan/lang/grammars/statement_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/expression07_grammar_inst.cpp -o stan/lang/grammars/expression07_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/statement_2_grammar_inst.cpp -o stan/lang/grammars/statement_2_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/term_grammar_inst.cpp -o stan/lang/grammars/term_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/indexes_grammar_inst.cpp -o stan/lang/grammars/indexes_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/semantic_actions_def.cpp -o stan/lang/grammars/semantic_actions_def.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/whitespace_grammar_inst.cpp -o stan/lang/grammars/whitespace_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/bare_type_grammar_inst.cpp -o stan/lang/grammars/bare_type_grammar_inst.o
g++ -std=gnu++14 -I"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -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"/usr/share/R/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'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include' -I'/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-OT058M/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c stan/lang/grammars/functions_grammar_inst.cpp -o stan/lang/grammars/functions_grammar_inst.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rstan.so chains.o pointer-tools.o stan_fit_base.o stanc.o Module.o stan_fit_rccp.o misc.o sparse_extractors.o init.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/term_grammar_inst.o stan/lang/grammars/indexes_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/local_var_decls_grammar_inst.o stan/lang/grammars/functions_grammar_inst.o -L/usr/lib/R/lib -lR
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: rstan.so] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/home/dlakelan/R/x86_64-pc-linux-gnu-library/4.0/rstan’
Is this me doing something wrong, like using an incompatible version of R or g++ or needing to install some development packages, or do I need to file a bug?