Thanks for sharing this with the community! This is exactly why I started this thread in order for everyone to share their experience and solutions to the various hiccups. It’s work to sort it out and more work to share that, but many will benefit.
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Worked for me too. Thanks!
If I try to fit a Stan model using CTRL+Enter in RStudio I get an error, but If I run it as a local job inside the RStudio IDE it works ok. That can also work as a solution.
Running on MacOs Catalina, R 4.0.0, with no .Makevars or .Rprofile.
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I have been having the same issues running RStan and the ~/.Rprofile still gave me an error message:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:82:
In file included from /usr/local/clang7/include/c++/v1/new:91:
In file included from /usr/local/clang7/include/c++/v1/exception:82:
In file included from /usr/local/clang7/include/c++/v1/cstdlib:86:
/usr/local/clang7/include/c++/v1/stdlib.h:94:15: fatal error: ‘stdlib.h’ file not found
#include_next <stdlib.h>
^~~~~~~~~~
1 error generated.
make: *** [file5e3542fec36.o] Error 1
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file5e3542fec36.cpp 2> file5e3542fec36.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection
I tried bgautijonsson’s run as local job solution, but it also gave me an error:
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
Trying to compile a simple C file
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -D_REENTRANT -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -include stan/math/prim/mat/fun/Eigen.hpp -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:88:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:613:1: error: unknown type name ‘namespace’
namespace Eigen {
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:613:16: error: expected ‘;’ after top level declarator
namespace Eigen {
^
;
In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:96:10: fatal error: ‘complex’ file not found
#include
^~~~~~~~~
3 errors generated.
make: *** [foo.o] Error 1
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from :1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:82:
In file included from /usr/local/clang7/include/c++/v1/new:91:
In file included from /usr/local/clang7/include/c++/v1/exception:82:
In file included from /usr/local/clang7/include/c++/v1/cstdlib:86:
/usr/local/clang7/include/c++/v1/stdlib.h:94:15: fatal error: ‘stdlib.h’ file not found
#include_next <stdlib.h>
^~~~~~~~~~
1 error generated.
make: *** [file69d1fe691b4.o] Error 1
Calls: sourceWithProgress … cxxfunctionplus -> -> cxxfunction -> compileCode
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file69d1fe691b4.cpp 2> file69d1fe691b4.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection
Calls: sourceWithProgress … eval -> stan -> stan_model -> cxxfunctionplus -> sink
Execution halted
Is there an additional step I should take for this to be fixed?
I believe the above is your problem. Remove anything in your paths where you point to clang7.
Thanks for this! Just a quick comment: R 4.0.1 has recently been released so getRversion() == "4.0.0" is now outdated - I would recommend to simply remove this part of the expression.
2 Likes
Thanks so much! Had the same problem, fix worked for me too with R version 4.0.1
Hello torkar,
I have a similar problem, now that I am trying to get the brms package running in R 4.0.5 on Mac Big Sur (OS 11.2.3). So, I thought, your advice might also work for me. Can you tell me what you mean, when you say " Remove anything in your paths where you point to clang7 . "? I do not know, how to do that, since the paths get called internally.
Best wishes,
Juliane