Hello Milani, Thank you very much for your e-mail. I was not aware of CmdStan and cmdstanr and will look into them. Meanwhile, I will continue using rstan 2.19.3.
Regarding Makevars, I am puzzled that now I have two Makevars files, both within the folder ~/Library/Frameworks/R.framework/Versions/4.0/Resources/library one sits in the folder RcppArmadillo/Skeleton and contains: ## With R 3.1.0 or later, you can uncomment the following line to tell R to ## enable compilation with C++11 (where available) ## ## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider ## availability of the package we do not yet enforce this here. It is however ## recommended for client packages to set it. ## ## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP ## support within Armadillo prefers / requires it CXX_STD = CXX11 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) the other, in folder RcppEigen/skeleton, has every line commented out: ## With Rcpp 0.11.0 and later, we no longer need to set PKG_LIBS as there is ## no user-facing library. The include path to headers is already set by R. #PKG_LIBS = ## With R 3.1.0 or later, you can uncomment the following line to tell R to ## enable compilation with C++11 (or even C++14) where available ## CXX_STD = CXX11 The Renviron file has a lot mor information. Since you tell me that none of these files are relevant for my problem now, I am inclined to forget abou them, but I am still curious as to what is their purpose. Best wishes, Gonçalo Gonçalo Ferraz Departamento de Ecologia, Instituto de Biociências Universidade Federal do Rio Grande do Sul http://ferrazlab.org/ <http://ferrazlab.org/> > On Nov 9, 2020, at 7:05 PM, Milani Chaloupka <m.chalou...@uq.edu.au> wrote: > > 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 > > http://mc-stan.org/cmdstanr/articles/cmdstanr.html > <http://mc-stan.org/cmdstanr/articles/cmdstanr.html> > > 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. > > regards > > Milani > > ____________________________________________________ > > 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.chalou...@uq.edu.au <mailto:m.chalou...@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@r-project.org <mailto:r-sig-mac@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. >> >> Gonçalo >> >>> On Nov 9, 2020, at 5:00 PM, Robert Goedman <goed...@icloud.com >>> <mailto:goed...@icloud.com>> wrote: >>> >>> Hi, >>> >>> 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. >>> > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
