Comments (11)
Closing this issue given its age, but feel free to re-open if it was never resolved.
Additionally, the github version of rstantools
now supports stan files comprised of only function definitions, which will be compiled and exported at installation.
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The bigger problem is that I'm trying to update my DeLorean
package to use the rstantools
recommended way to pre-compile models to fix some recent CRAN warnings/errors and I'm hitting this error there as well. See this branch: https://github.com/JohnReid/DeLorean/tree/stan-update
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I called rstan_package_skeleton
in order to see the boilerplate code required to implement pre-compiled models. It sounds like you are suggesting a more direct way of updating DeLorean. Regardless of how I update DeLorean, following the vignette shouldn't produce the error message. In fact I get the same error message when I copy the boilerplate code over to the DeLorean branch. This makes me believe there is something wrong in my set up but I have not been able to work out what it is. I updated StanHeaders, rstan and rstan_tools but that didn't help.
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Great. Thanks for your help. I'll keep plugging away.
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I've followed the vignette through to the end. I have uncovered another problem. I need to expose some functions from my Stan code to R and this doesn't seem to be working as it should. I add a function to the top of lm.stan
in the vignette, re-build the package and then get:
> model <- stanmodels[['lm']]
> message(class(model))
stanmodel
> expose_stan_functions(model)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘get_stancode’ for signature ‘"stanmodel"’
but the expose_stan_functions
explicitly says I should be able to pass a stanmodel
in. Something pretty similar was working with my original set up so maybe it is to do with pre-compiled models?
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I would be happy passing the path to the lm.stan
model description into expose_stan_functions
but this is not installed with the package. Is this easy to do?
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Or maybe it is easy to compile the functions and expose them at package installation time?
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The expose_stan_functions() function is more intended for runtime. The binary it produces may not work on another computer. It is probably better to generate the C++ for the functions you want to expose once and then compile that as if you had written it by hand. @wds15 has gone through this process before I think.
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Just a quick note from my side, I run into the same problem that exposing the stan functions from a package is rather tricky. I first thought it might be an option to generate the code using expose_stan_functions
copy the source to the package and then run compileAttributes
. This does not work, nor anything else that works. It would be great if there would be an example how to approach this best.
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Related Issues (20)
- GHA failure of new standalone functions checks HOT 1
- Problem with line endings in automatically generated src/ files HOT 1
- Problems with compiling mixutre models on Windows (rstantools 2.3.0) HOT 4
- auto detect need for recompile? HOT 9
- Auto-format Stan models during rstan_config()? HOT 5
- Slow package building with rstan 2.26.23
- automatically exposing functions from Stan to R
- write_stan_json and to_stan_json to rstantools? HOT 6
- add posterior_epred generic
- include problem with some versions of rstantools 2.x and/or StanHeaders HOT 43
- errors if user model is called base.stan HOT 1
- Are ALL stan models recompiled when a package is updated? HOT 3
- LoadLibrary failure for Prophet on Windows HOT 11
- configure files in packages made with rstan_create_package() produces a note when running R CMD check HOT 3
- switch to github actions for CI
- don't create travis.yml
- Github actions workflow - test against rstan experimental or preview? HOT 2
- Backwards compatibility issue with model names HOT 1
- rstantools cannot find `stan/version.hpp` HOT 6
- R CMD check NOTE about Imports: RcppParallel HOT 5
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