Error using brms on RHEL

Interfaces brms
1

Please also provide the following information in addition to your question:

  • Operating System: Red Hat Enterprise Linux 7.7
  • brms Version:2.10.0

I’m trying to run the basic example in brms on our departmental server, but it keeps throwing an error. I’m on R version 3.6.0. My .Makevars file is:
CXX14 = g++ -std=c++1y
MAKEFLAGS = -j4
CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX11FLAGS=-O3 -march=native

The error is given below.
Any help would be appreciated

data(epilepsy)
fit1 ← brm(count ~ zAge + zBase * Trt + (1|patient),

  •         data = epilepsy, family = poisson())

Compiling the C++ model
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/BH/include/boost/random/detail/int_float_pair.hpp:26,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/BH/include/boost/random/exponential_distribution.hpp:27,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/BH/include/boost/random/gamma_distribution.hpp:25,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:292,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command ‘/usr/lib64/R/bin/R CMD SHLIB file7a5dcf0de10.cpp 2> file7a5dcf0de10.cpp.err.txt’ had status 1
Error in sink(type = “output”) : invalid connection

2

My guess is that your C++ compiler is too old. What is the error message (starts with error:) when you do

example(stan_model, package = "rstan", run.dontrun = TRUE)

?

3

That throws the eventual error:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /usr/include/c++/4.8.2/type_traits:35:0,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/is_constant.hpp:4,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/arr/meta/is_constant_struct.hpp:4,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/mat/meta/is_constant_struct.hpp:4,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/mat.hpp:15,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /storage01/users/ozd504/R/x86_64-redhat-linux-gnu-library/3.6/StanHeaders/include/stan/math.hpp:4,
from /storage01/us

4

We need the part that starts with error: but I can tell from the 4.8.2 stuff that the error is that C++14 is not supported.

5

Thank you, the first error I see is:
error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.

6

Right. It actually needs to be C++14 to work with Stan. You need
https://developers.redhat.com/products/developertoolset/overview

7

Thank you Ben, i’ve contacted my sys admin.

8

Sorry, one more question from my sys admin, what version of linux do you use to develop Stan?

9

We don’t develop Stan on or for any particular operating system. You just need a compiler that supports the C++14 standard. On Linux, that is going to be g++ version 5 or later or clang++ version 4 or later.

10

We installed the developer tools and now everything works as it should, thanks again for the help