Model compile apparent error in the getting started but fitting is successful?

[athowes]

The getting started vignette has a bug on main currently, see here, or:

fit <- epidist(
  data = data, chains = 2, cores = 2, refresh = ifelse(interactive()), 250, 0)
)
#> Running /opt/R/4.4.2/lib/R/bin/R CMD SHLIB foo.c
#> using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
#> gcc -I"/opt/R/4.4.2/lib/R/include" -DNDEBUG   -I"/home/runner/work/_temp/Library/Rcpp/include/"  -I"/home/runner/work/_temp/Library/RcppEigen/include/"  -I"/home/runner/work/_temp/Library/RcppEigen/include/unsupported"  -I"/home/runner/work/_temp/Library/BH/include" -I"/home/runner/work/_temp/Library/StanHeaders/include/src/"  -I"/home/runner/work/_temp/Library/StanHeaders/include/"  -I"/home/runner/work/_temp/Library/RcppParallel/include/"  -I"/home/runner/work/_temp/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 '/home/runner/work/_temp/Library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/usr/local/include    -fpic  -g -O2  -c foo.c -o foo.o
#> In file included from /home/runner/work/_temp/Library/RcppEigen/include/Eigen/Core:19,
#>                  from /home/runner/work/_temp/Library/RcppEigen/include/Eigen/Dense:1,
#>                  from /home/runner/work/_temp/Library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22,
#>                  from <command-line>:
#> /home/runner/work/_temp/Library/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: cmath: No such file or directory
#>   679 | #include <cmath>
#>       |          ^~~~~~~
#> compilation terminated.
#> make: *** [/opt/R/4.4.2/lib/R/etc/Makeconf:195: foo.o] Error 1

Looks to be to do with Stan versions ("fatal error: cmath: No such file or directory").

Edit: doesn't happen with cmdstanr backend so an rstan problem.

[athowes]

Looks related (both fatal to do with cmath) to my report in #526 (comment).

[seabbs]

it doesnt exist in the CI so I think its a caching failure. I am not sure why the cache is on

[seabbs]

I see that this isnt blocking a fit from happening as the fit object is present with or without caching so it must be a compile warning vs fit. I have edited the title to reflect this

[athowes]

I have a similar issue locally. Initially was discussed on #526:

I downgraded rstan to:

> packageVersion("rstan")
[1] ‘2.32.6’

and used:

> packageVersion("primarycensored")
[1] ‘1.1.0.1000’

Doing this and trying to run the model I get a pop-up:

If I press "Yes" then it hangs at for a while:

Then eventually it runs and fits OK.

The next time I run the code, it asks me again if I'd like to install the build tools.

This looks like it would explain the results in #532 (there is a compile error, but eventually it runs).

[seabbs]

As in the other thread can you check the cran version of primarycensored?

[athowes]

As in the other thread can you check the cran version of primarycensored?

Yep with CRAN version of primarycensored (primarycensored_1.1.0) then it was OK.

[seabbs]

Hmm tricky. I can look at this more but my expectation is that this is related to the build tools (i.e it should show up if forcing the install from CRAN to be from source). We have had a flag from CRAN that rstan is throwing a warning/error somewhat like this for all CRAN rstan based packages which I expect will get resolved pretty quick so I would think this should be transcient. I think given that I am going to take no action for a week or so and see where we are? As this doesn't stop models actually being fit that seems like it wont block anything?