'cmath' file not found when running brms models

Interfaces brms
,
1

Short summary of the problem

I encountered an error message while running the model with the following codes.

m2 <- brm(response_rating~ cond + (1 + cond|item_id) + (1 + cond|participant), data = df_analysis1, family = cumulative(link="logit", threshold="flexible"), init = 0, chains = 4, iter = 4000)

Here is the error message:

Compiling Stan program...
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.4)’
using SDK: ‘’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/unsupported"  -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/src/"  -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include/"  -I"/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
In file included from <built-in>:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/Core:19:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
  679 | #include <cmath>
      |          ^~~~~~~
1 error generated.
make: *** [foo.o] Error 1

But after this message, the model seems to continue running with good results. I was wondering how to get rid of this ‘cmath’ file not found error.

  • Operating System: macOS Sequoia 15.1
  • brms Version: 2.22.0
  • R version 4.4.2
  • Platform: aarch64-apple-darwin20

Thank you very much for the help!

2

This sounds similar to RcppEigen, cmath, and rstan installation issues - #3 by turtlegraphics

If so, the issue is likely that your version of XCode is out of sync with your operating system version

1 Like
3

Thank you @WardBrian for the suggestion. I’ve solved the issue by installing the latest XCode with the latest OS system (Sequoia). Now brms can successfully compile and model my data!

3 Likes
4

I hit this issue, too. After installing the latest XCode with Sequoia, I’m still seeing the issue. I restarted R, and Mac OS, but the error remains.

@claire, was there anything else you had to do to get it to work?