afni.nimh.nih.gov
| January 10, 2019 04:54AM | |
Registered: 9 years ago Posts: 202 |
Thanks Gang, I saw that when troubleshooting. But I can't seem to make it work. It feels like R does not find what's in the file since, for every thing I have tried, I still get
1. Just uncomment CXX_STD = CXX11 then start R and tried installing
2. Uncomment and change it to CXX_STD = CXX14 then start R and tried installing
3. Keep the comment and added (tried seperatley):
a) CXX14 = g++
CXX14FLAGS = -O3
b) CXX14 = clang++
CXX14FLAGS = -O3
c) CXX14 = g++ -std=c++1y (from the git-link)
4. Then I commented everything and copied the file to ~/R/Makevars and tried all the combinations above.
This did not set the CXX14 value for R. I can see that here:
So I edited the /usr/lib64/R/etc/Malkeconf file instead where I filled out these previously empty lines:
Now R gets those variables:
Now I don't get the same error, now it tries to compile when I install "brms". But it failes because it can't install "rstan". So I try to install "rstan" (which before also failed because of " C++14 standard requested but CXX14 is not defined"). This tries to compile but the compilation failes. There is alot of terminal output but this section is repeated many many times:
I also tried (from the web) to set
CXX14STD = -std=gnu++14 which gives an error about gnu++14 is not a valid option. I found out that on older gcc versions you had to type -std=c++1y instead of gnu++14. This did not complain about the option and ran. But again the compilation fails. So when adding CXX14STD = -std=c++1y the output changes (from aboive) to
If this was ubuntu I could just have run
sudo apt-get install r-cran-rstan
sudo apt-get install r-cran-shinystan
sudo apt-get install r-cran-brms
But since I'm stuck with CentOS and can't find a similar yum command I'm stuck with making this work :(
Thanks!
Edited 7 time(s). Last edit at 01/10/2019 09:00AM by Robin.
Error in .shlib_internal(args) : C++14 standard requested but CXX14 is not definedFirst off all, I only found the Makevars file here (not in ~/R/Makevars):
~/R/RcppEigen/skeleton/MakevarsThe file looked like this:
## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is ## no user-facing library. The include path to headers is already set by R. #PKG_LIBS = ## With R 3.1.0 or later, you can uncomment the following line to tell R to ## enable compilation with C++11 (or even C++14) where available #CXX_STD = CXX11So I tried the following:
1. Just uncomment CXX_STD = CXX11 then start R and tried installing
2. Uncomment and change it to CXX_STD = CXX14 then start R and tried installing
3. Keep the comment and added (tried seperatley):
a) CXX14 = g++
CXX14FLAGS = -O3
b) CXX14 = clang++
CXX14FLAGS = -O3
c) CXX14 = g++ -std=c++1y (from the git-link)
4. Then I commented everything and copied the file to ~/R/Makevars and tried all the combinations above.
This did not set the CXX14 value for R. I can see that here:
[robka@n238-192-238 etc]$ R CMD config CXX11 g++ -m64 [robka@n238-192-238 etc]$ R CMD config CXX11FLAGS -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic [robka@n238-192-238 etc]$ R CMD config CXX14 [robka@n238-192-238 etc]$ R CMD config CXX14FLAGS [robka@n238-192-238 etc]$
So I edited the /usr/lib64/R/etc/Malkeconf file instead where I filled out these previously empty lines:
CXX14 = g++ CXX14FLAGS = -O3 CXX14PICFLAGS = CXX14STD =
Now R gets those variables:
[robka@n238-192-238 etc]$ R CMD config CXX14 g++ [robka@n238-192-238 etc]$ R CMD config CXX14FLAGS -O3
Now I don't get the same error, now it tries to compile when I install "brms". But it failes because it can't install "rstan". So I try to install "rstan" (which before also failed because of " C++14 standard requested but CXX14 is not defined"). This tries to compile but the compilation failes. There is alot of terminal output but this section is repeated many many times:
In file included from /home/robka/R/StanHeaders/include/src/stan/lang/ast.hpp:65:0,
from /home/robka/R/StanHeaders/include/src/stan/lang/ast_def.cpp:7,
from lang__ast_def.cpp:18:
/home/robka/R/StanHeaders/include/src/stan/lang/ast/sigs/function_signatures.hpp:306:17: note: template<class T> stan::lang::expr_type stan::lang::function_signatures::rng_return_type(const stan::lang::expr_type&, const stan::lang::expr_type&, const stan::lang::expr_type&)
expr_type rng_return_type(const expr_type& t,
^
/home/robka/R/StanHeaders/include/src/stan/lang/ast/sigs/function_signatures.hpp:306:17: note: template argument deduction/substitution failed:
In file included from /home/robka/R/StanHeaders/include/src/stan/lang/ast/sigs/function_signatures_def.hpp:486:0,
from /home/robka/R/StanHeaders/include/src/stan/lang/ast_def.cpp:119,
from lang__ast_def.cpp:18:
/home/robka/R/StanHeaders/include/src/stan/lang/function_signatures.h:1366:57: note: cannot convert ‘t’ (type ‘const int’) to type ‘const stan::lang::expr_type&’
add("weibull_rng", rng_return_type<double_type>(t, u), t, u);
And at the end:
make: *** [lang__ast_def.o] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/home/robka/R/rstan’
The downloaded source packages are in
‘/tmp/Rtmp291Q9L/downloaded_packages’
Warning message:
In install.packages("rstan") :
installation of package ‘rstan’ had non-zero exit status
I feel this is kind of over my head. I have g++/gcc available form the terminal to they are installed. But I don't know how the /usr/lib64/R/etc/Malkeconf file should be altered.
I also tried (from the web) to set
CXX14STD = -std=gnu++14 which gives an error about gnu++14 is not a valid option. I found out that on older gcc versions you had to type -std=c++1y instead of gnu++14. This did not complain about the option and ran. But again the compilation fails. So when adding CXX14STD = -std=c++1y the output changes (from aboive) to
> install.packages("rstan")
Installing package into ‘/home/robka/R’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL '[ftp.acc.umu.se];
Content type 'application/x-gzip' length 838052 bytes (818 KB)
==================================================
downloaded 818 KB
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c chains.cpp -o chains.o
In file included from /home/robka/R/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/robka/R/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/robka/R/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/robka/R/BH/include/boost/random/linear_congruential.hpp:30,
from /home/robka/R/BH/include/boost/random/additive_combine.hpp:27,
from chains.cpp:29:
/home/robka/R/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c init.cpp -o init.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__ast_def.cpp -o lang__ast_def.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__bare_type_grammar_inst.cpp -o lang__grammars__bare_type_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__expression07_grammar_inst.cpp -o lang__grammars__expression07_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__expression_grammar_inst.cpp -o lang__grammars__expression_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__functions_grammar_inst.cpp -o lang__grammars__functions_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__indexes_grammar_inst.cpp -o lang__grammars__indexes_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__program_grammar_inst.cpp -o lang__grammars__program_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__semantic_actions.cpp -o lang__grammars__semantic_actions.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__statement_2_grammar_inst.cpp -o lang__grammars__statement_2_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__statement_grammar_inst.cpp -o lang__grammars__statement_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__term_grammar_inst.cpp -o lang__grammars__term_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__var_deccls_grammar_inst.cpp -o lang__grammars__var_deccls_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c lang__grammars__whitespace_grammar_inst.cpp -o lang__grammars__whitespace_grammar_inst.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c misc.cpp -o misc.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c pointer-tools.cpp -o pointer-tools.o
In file included from /home/robka/R/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /home/robka/R/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from /home/robka/R/BH/include/boost/random/detail/const_mod.hpp:23,
from /home/robka/R/BH/include/boost/random/linear_congruential.hpp:30,
from /home/robka/R/BH/include/boost/random/additive_combine.hpp:27,
from pointer-tools.cpp:2:
/home/robka/R/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c sparse_extractors.cpp -o sparse_extractors.o
g++ -std=c++1y -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"`"/usr/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/robka/R/Rcpp/include" -I"/home/robka/R/RcppEigen/include" -I"/home/robka/R/BH/include" -I"/home/robka/R/StanHeaders/include" -I/usr/local/include -O3 -c stanc.cpp -o stanc.o
g++ -std=c++1y -shared -L/usr/lib64/R/lib -Wl,-z,relro -o rstan.so chains.o init.o lang__ast_def.o lang__grammars__bare_type_grammar_inst.o lang__grammars__expression07_grammar_inst.o lang__grammars__expression_grammar_inst.o lang__grammars__functions_grammar_inst.o lang__grammars__indexes_grammar_inst.o lang__grammars__program_grammar_inst.o lang__grammars__semantic_actions.o lang__grammars__statement_2_grammar_inst.o lang__grammars__statement_grammar_inst.o lang__grammars__term_grammar_inst.o lang__grammars__var_deccls_grammar_inst.o lang__grammars__whitespace_grammar_inst.o misc.o pointer-tools.o sparse_extractors.o stanc.o -L/usr/lib64/R/lib -lR
/usr/bin/ld: chains.o: relocation R_X86_64_32 against hidden symbol `_ZGVZ7dataptrP7SEXPRECE3fun' can not be used when making a shared object
/usr/bin/ld: init.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__ast_def.o: relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__bare_type_grammar_inst.o: relocation R_X86_64_32 against symbol `_ZN5boost9function4IbRNS_6spirit17line_pos_iteratorIN9__gnu_cxx17__normal_iteratorIPKcSsEEEERKS8_RNS1_7contextINS_6fusion4consIRNS1_11unused_typeENSD_4nil_EEENSD_6vectorIIEEEEERKSF_E5dummy7nonnullEv' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__expression07_grammar_inst.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__expression_grammar_inst.o: relocation R_X86_64_32 against symbol `_ZN5boost9function4IbRNS_6spirit17line_pos_iteratorIN9__gnu_cxx17__normal_iteratorIPKcSsEEEERKS8_RNS1_7contextINS_6fusion4consIRNS1_11unused_typeENSD_4nil_EEENSD_6vectorIIEEEEERKSF_E5dummy7nonnullEv' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__functions_grammar_inst.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__indexes_grammar_inst.o: relocation R_X86_64_32 against symbol `_ZN5boost9function4IbRNS_6spirit17line_pos_iteratorIN9__gnu_cxx17__normal_iteratorIPKcSsEEEERKS8_RNS1_7contextINS_6fusion4consIRNS1_11unused_typeENSD_4nil_EEENSD_6vectorIIEEEEERKSF_E5dummy7nonnullEv' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__program_grammar_inst.o: relocation R_X86_64_32 against symbol `_ZN5boost9function4IbRNS_6spirit17line_pos_iteratorIN9__gnu_cxx17__normal_iteratorIPKcSsEEEERKS8_RNS1_7contextINS_6fusion4consIRNS1_11unused_typeENSD_4nil_EEENSD_6vectorIIEEEEERKSF_E5dummy7nonnullEv' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__semantic_actions.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__statement_2_grammar_inst.o: relocation R_X86_64_32 against symbol `_ZN5boost9function4IbRNS_6spirit17line_pos_iteratorIN9__gnu_cxx17__normal_iteratorIPKcSsEEEERKS8_RNS1_7contextINS_6fusion4consIRNS1_11unused_typeENSD_4nil_EEENSD_6vectorIIEEEEERKSF_E5dummy7nonnullEv' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__statement_grammar_inst.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__term_grammar_inst.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__var_deccls_grammar_inst.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: lang__grammars__whitespace_grammar_inst.o: relocation R_X86_64_32S against symbol `_ZTIN5boost6spirit2qi6detail13parser_binderINS1_11alternativeINS_6fusion4consINS1_15expect_operatorINS6_INS1_8sequenceINS6_INS1_14omit_directiveINS1_14literal_stringIRA3_KcLb1EEEEENS6_INS1_6kleeneINS1_10differenceINS1_10char_classINS0_3tag9char_codeINSJ_5char_ENS0_13char_encoding8standardEEEEESE_EEEENS5_4nil_EEEEEEENS6_ISF_SS_EEEEEENS6_INS8_INS6_ISF_NS6_INSG_INSH_ISP_NS1_10eol_parserEEEEESS_EEEEEENS6_INS1_6actionINS8_INS6_INS9_INS1_12literal_charISN_Lb1ELb0EEEEES12_EEEENS_7phoenix5actorINS_5proto7exprns_10basic_exprINS1B_6detail3tag13function_evalENS1D_7argsns_5list2INS1F_INS1D_6tagns_3tag8terminalENS1J_4termIN4stan4lang23deprecate_pound_commentEEELl0EEENS1C_INS1F_IS1N_NS1O_INS_17reference_wrapperISt18basic_stringstreamIcSt11char_traitsIcESaIcEEEEEELl0EEEEEEELl2EEEEEEENS6_INSI_INSK_INSJ_5spaceENSM_5asciiEEEEESS_EEEEEEEEEEN4mpl_5bool_ILb0EEEEE' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: pointer-tools.o: relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: sparse_extractors.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: stanc.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
make: *** [rstan.so] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/home/robka/R/rstan’
The downloaded source packages are in
‘/tmp/RtmpaR03U1/downloaded_packages’
Warning message:
In install.packages("rstan") :
installation of package ‘rstan’ had non-zero exit status
The same error occurs if I cange it to CXX14STD = -std=gnu++1y (pretty much identically)
If this was ubuntu I could just have run
sudo apt-get install r-cran-rstan
sudo apt-get install r-cran-shinystan
sudo apt-get install r-cran-brms
But since I'm stuck with CentOS and can't find a similar yum command I'm stuck with making this work :(
Thanks!
Edited 7 time(s). Last edit at 01/10/2019 09:00AM by Robin.
| Subject | Author | Posted |
|---|---|---|
|
Robin | January 09, 2019 09:52AM |
|
gang | January 09, 2019 10:35AM |
|
Robin | January 10, 2019 04:54AM |
|
gang | January 10, 2019 06:29PM |
|
Robin | January 11, 2019 07:33AM |
|
gang | January 14, 2019 03:00PM |
