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biodiverse / ubms

Fit models to data from unmarked animals using Stan. Uses a similar interface to the R package 'unmarked', while providing the advantages of Bayesian inference and allowing estimation of random effects.
https://hmecology.github.io/ubms/
GNU General Public License v3.0
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Compatibility with next rstan #48

Closed andrjohns closed 3 years ago

andrjohns commented 3 years ago

Hi,

This PR adds the changes to build flags that are needed for compatibility with the upcoming release of rstan. These changes include adding compiler & linker flags needed for working with StanHeaders >= 2.26, namely the addition of the TBB (RcppParallel).

Additionally, this PR adds a compiler flag to your Makevars files which is needed for compatibility with the upcoming version of rstan: -DUSE_STANC3

The Stan-to-c++ transpiler (stanc) was refactored after 2.21, and so different c++ is used in the new rstan package (>= 2.26). Because of this, the flag -DUSE_STANC3 needs to be added when a stan model is being run using the new rstan package (and the new stanc implementation).

Feel free to let me know if you need any more info.

Thanks! Andrew

codecov-commenter commented 3 years ago

Codecov Report

Merging #48 (bd63a96) into master (527648f) will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #48   +/-   ##
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  Coverage   98.94%   98.94%           
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  Files          30       30           
  Lines        1807     1807           
=======================================
  Hits         1788     1788           
  Misses         19       19

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kenkellner commented 3 years ago

Thank you!