Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Installation requires workarounds #7

Open
jim-sheldon opened this issue May 22, 2024 · 0 comments
Open

Installation requires workarounds #7

jim-sheldon opened this issue May 22, 2024 · 0 comments

Comments

@jim-sheldon
Copy link
Contributor

jim-sheldon commented May 22, 2024

Following installation instructions and running on Mac OS yields /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:9:10: fatal error: 'tbb/tbb_stddef.h' file not found.

Got around this by copy/pasting PKG_LIBS and PKG_CPPFLAGS from the output of example(stan_model, package = "rstan", run.dontrun = TRUE, verbose=TRUE) to Makevars. This works in the Docker image build too.

It looks like those values change depending on the operating system, and need to exist in Makevars before installation...perhaps something like sed could do this?

Another problem: the output of min ( int, int ); in the .stan files returns real.

The quick fix in src/stan_files/symptom_report_model.stan, line 95:

int ddxx_left = min( ddxx, t_rep_symptoms );
ddxx = max( ddxx_left, 1 );
int sdxx_left = min( ll_symptoms[idx] + t_symptom_pre, t_max );
sdxx = max( sdxx_left, 1 );

And in src/stan_files/symptom_report_model_gamma.stan, line 83:

int ddxx_left = min( ddxx, t_rep_symptoms );
ddxx = max( ddxx_left, 1 );
int sdxx_left = min( ll_symptoms[idx] + t_symptom_pre, t_max );
sdxx = max( sdxx_left, 1 );
@jim-sheldon jim-sheldon changed the title Makevars support for different environments Installation requires workarounds May 22, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant