Deep Copy Issue

Interfaces brms
1

I went to re-run a model (it had successful run before, but had 2 divergent transitions), I am suddenly getting this output:

“DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=theta1) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.”

This Info message is copied 4 times with different variable names, and this chunk of notes prints once before, and once after the “Compiling the C++ model” line.

Ultimately, it’s also failing to compile:

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created!

and then a list of paths.

Any thoughts about what is going wrong?
What does the Info message mean?

The model I am running is:

fit1_v4 ← brm(brmsformula(
intervals ~ 1 + phase +(1|male|male_id),
theta2 ~ 1 + phase + (1|male|male_id)),
data=filtered_data,
family=mixture(Gamma(“log”), Gamma(“log”), order=TRUE),
prior = prior1,
control = list(adept_delta = 0.99),
warmup = 1000,
iter = 4000,
chains = 2,
cores = 2)

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

  • Operating System: Windows 8.1
  • brms Version: 2.5.0
2

Those deep copy things should not cause a compiler error. What is the rest of the compiler error message?

3

The full compilation errors are:

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from C:/Users/Ryane/Documents/R/win-library/3.5/BH/include/boost/config.hpp:39:0,
from C:/Users/Ryane/Documents/R/win-library/3.5/BH/include/boost/math/tools/config.hpp:13,
from C:/Users/Ryane/Documents/R/win-library/3.5/StanHeaders/include/stan/math/rev/core/var.hpp:7,
from C:/Users/Ryane/Documents/R/win-library/3.5/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5,
from C:/Users/Ryane/Documents/R/win-library/3.5/StanHeaders/include/stan/math/rev/core.hpp:12,
from C:/Users/Ryane/Documents/R/win-library/3.5/StanHeaders/include/stan/math/rev/mat.hpp:4,
from C:/Users/Ryane/Documents/R/win-library/3.5/StanHeaders/include/stan/math.hpp:4,
from C:/Users/Ryane/Documents/R/win-library/3.5/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file142cd6e38e9.cpp:8:
In addition: Warning messages:
1: In rstan::stan_model(model_code = x$model, save_dso = save_dso) :
StanHeaders version is ahead of rstan version; update to latest rstan
2: In system(cmd, intern = !verbose) :
running command ‘C:/PROGRA~1/R/R-35~1.0/bin/x64/R CMD SHLIB file142cd6e38e9.cpp 2> file142cd6e38e9.cpp.err.txt’ had status 1

4

Most likely this

5

Ok, I’m working on the rstan issue (unsurprisingly, this issue started after I updated my packages).

Do you have further information a bout the deep copy information? It’s not a warning, but I’m not sure what it means?

Thanks for the help on the compilation problem!

6

It is just that brms is generating some Stan code that does extra copying but the posterior distribution is unaffected. As a user, you can’t do anything about it unless you edit the generated code.

7

Ok that’s reassuring - doesn’t sound like something I need to worry about!
Thanks again for your help.