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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| 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 |
