[R-SIG-Mac] Rstan compilation hangs misterisouly

Milani Chaloupka m@ch@|oupk@ @end|ng |rom uq@edu@@u
Mon Nov 9 23:05:15 CET 2020

Hi Goncalo

The issue, as I pointed out to you yesterday on Stan Discourse, is rstan (the interface to Stan via R).

And hence my advice to you there was to downgrade to Stan 2.19.3

It was not your Makevars file - although that was an incomplete Makevars you had if there were in fact no typos in your previous email.

As others have pointed out, a Makevars file is no longer necessary to run Stan if using MACOS X Catalina onwards.

Nor is the Renviron file.

Do not upgrade to any rstan higher than 2.19.3 until the rstan issues on various platforms are resolved.

Meanwhile, you can use, as is my preference, the CmdStan and cmdstanr interface to Stan instead of rstan, which …

(1) samples quite a bit faster than rstan

(2) is more up-to-date with Stan although with a few less features than rstan


And if you are using the brms interface to Stan then it also has an option in the brm() function to use cmdstanr as the backend rather than rstan.




Dr Milani Chaloupka
Ecological Modelling Services P/L
PO Box 6150, University of Queensland
St Lucia, Queensland, 4067, Australia

Honorary Associate Professor
School of Biological Sciences, University of Queensland
Brisbane, Queensland, 4072, Australia

Scientific Advisory Committee (Member)
Caribbean Conservation Corporation
Gainesville, Florida, USA

Science and Statistics Committee (Member)
Western Pacific Regional Fisheries Management Council
NOAA, US Dept of Commerce, Honolulu, Hawaii, USA

m.chaloupka using uq.edu.au<mailto:m.chaloupka using uq.edu.au>
mobile: (local) 0419180554  (international) + 61 419180554
skype: milani2005

On 10 Nov 2020, at 6:03 am, Goncalo Ferraz via R-SIG-Mac <r-sig-mac using r-project.org<mailto:r-sig-mac using r-project.org>> wrote:

Hi, This is helpful information. Thank you. Meanwhile, I tried reverting to version 2.19.3 of rstan and it does not hang on me. I couldn’t yet understand what is going on with the most recent version, but at least for now I can work.


On Nov 9, 2020, at 5:00 PM, Robert Goedman <goedman using icloud.com<mailto:goedman using icloud.com>> wrote:


Not sure if this helps and/or is even related but since about 2 months I have not been able to get rstan to work inside the R-GUI. Like you describe, it hangs and never returns. I don’t use rstan directly but use ulam() in the `rethinking` package to very occasionally check the Stan language program generated by ulam() after running it.

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