Thank you very much John. I restarted my computer, and everything looks fine now, I fitted a brms model without the error message.
Manuel El sáb., 14 dic. 2019 a las 19:45, Fox, John (<j...@mcmaster.ca>) escribió: > Dear Manuel, > > As far as I can tell, a lot of people are experiencing problems with rstan > under Catalina -- I don't use brms but rather rstan directly, and I > thrashed around quite a bit to get it work reliably (at least so far!). > > The final bit of the puzzle for me was to modify Makevars in the .R > subdirectory of my home directory according to the instructions at < > https://discourse.mc-stan.org/t/dealing-with-catalina-ii/11802/74>. Maybe > that will work for you too. If this is in fact a generally satisfactory > solution, one would hope that it could be made more convenient for macOS > rstan users. > > I hope this helps, > John > > ----------------------------- > John Fox, Professor Emeritus > McMaster University > Hamilton, Ontario, Canada > Web: http::/socserv.mcmaster.ca/jfox > > > On Dec 14, 2019, at 6:28 PM, Manuel Spínola <mspinol...@gmail.com> > wrote: > > > > Dear list members, > > > > I updated everything, Catalina, Xcode, CLT, R 3.6.2, rstan from source, > and > > installed the r-macos-rtools, but I still have problems. > > > > library(brms) > > group <- rep(c("treat", "placebo"), each = 30) > > symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = 0, sd = > 1)) > > dat1 <- data.frame(group, symptom_post) > > > > fit1 <- brm(bf(symptom_post ~ group, sigma ~ group), > > data = dat1, family = gaussian()) > > > > Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup) > > [1] "Error in sampler$call_sampler(args_list[[i]]) : " > > [2] " c++ exception (unknown reason)" > > error occurred during calling the sampler; sampling not done > > > > > > > > > > > > > > El jue., 12 dic. 2019 a las 12:51, Balamuta, James Joseph (< > > balam...@illinois.edu>) escribió: > > > >> Greetings and Salutations All, > >> > >> Great to see the `r-macos-rtools` installer popping up! As the author of > >> it, please note that it's an unofficial (non-CRAN backed) installer that > >> seeks to automatically establish the CRAN toolchain in a friendly GUI > >> installer. We developed it to help out students in STAT 385 @ UIUC [ > >> http://stat385.com/ ] setup the correct developer environment in a > >> uniform manner as there wasn't really any prior installer packages made > >> available at the time. We're grateful for the financial support that was > >> given by Timothy Bates to sign the installer. > >> > >> With this being said, each step the installer takes is documented > across a > >> README file, installer splash screen, and by a post. > >> > >> README Overview: > >> https://github.com/rmacoslib/r-macos-rtools#what-does-the-installer-do > >> Installer Splash: > >> > https://raw.githubusercontent.com/rmacoslib/r-macos-rtools/master/readme_img/lock_icon.png > >> Post: > >> > https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ > >> > >> That said, there is also Appendix C.3 macOS of R Installation and > >> Administration [ > >> https://cran.r-project.org/doc/manuals/r-release/R-admin.html#macOS ] > >> that goes over the details in greater depth. > >> > >> For those who are worried about security, please note that we've taken > >> steps to ensure secure downloads by verifying the installer hashes > prior to > >> installing per prior remarks by Simon regarding earlier versions of the > >> installer [ see the prior discussion and my response here: > >> https://stat.ethz.ch/pipermail/r-sig-mac/2018-May/012745.html ]. > >> > >> Lastly, and perhaps more critically, please note that just using Xcode > CLI > >> is not sufficient as it does not match the prescribed compilation > toolchain > >> (clang7 with OpenMP enabled and gfortran). > >> > >> Best, > >> > >> JJB > >> > >> On 12/11/19, 7:25 PM, "R-SIG-Mac on behalf of Manuel Spínola" < > >> r-sig-mac-boun...@r-project.org on behalf of mspinol...@gmail.com> > wrote: > >> > >> An update. > >> > >> Before doing the suggested installation, I updated Catalina to > 10.5.2, > >> Xtools to 11.3 and the Command Line Tools and it works. > >> > >> Manuel > >> > >> El mié., 11 dic. 2019 a las 16:05, Ken Beath (<k...@kjbeath.com.au>) > >> escribió: > >> > >>> No, it only downloads and installs the right compilers and updates > >>> Makevars and REnvirons. These are what Stan and RCpp require so you > >> could > >>> do these manually. > >>> > >>> What it does is described at > >> https://github.com/rmacoslib/r-macos-rtools > >>> > >>> Ken > >>> > >>>> On 12 Dec 2019, at 1:14 am, Manuel Spínola <mspinol...@gmail.com> > >> wrote: > >>>> > >>>> Thank you very much to all. > >>>> > >>>> Does Installing the macos-rtools could affect R in other ways? > >>>> > >>>> Manuel > >>>> > >>>> El mié., 11 dic. 2019 a las 6:56, Ken Beath (<k...@kjbeath.com.au>) > >>> escribió: > >>>> What worked for me was installing the tools using > >>> https://github.com/rmacoslib/r-macos-rtools/releases > >>>> > >>>> and then installing rstan from source ie > >>> install.packages(“rstan”,type=“source) as suggested on one of the > >> stan > >>> forums > >>>> > >>>> Ken > >>>> > >>>>> On 11 Dec 2019, at 11:09 am, Manuel Spínola < > >> mspinol...@gmail.com> > >>> wrote: > >>>>> > >>>>> Dear list members, > >>>>> > >>>>> When trying to fit this example from the CRAN repository fro > >> brms, I > >>> got > >>>>> the following error message after the 4th chain. I am using R > >> 3.6.1 in > >>>>> Catalina MacOS. > >>>>> > >>>>> > >>>>> library(brms) > >>>>> > >>>>> group <- rep(c("treat", "placebo"), each = 30) > >>>>> symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean = > >> 0, sd > >>> = 1)) > >>>>> dat1 <- data.frame(group, symptom_post) > >>>>> > >>>>> fit1 <- brm(bf(symptom_post ~ group, sigma ~ group), > >>>>> data = dat1, family = gaussian()) > >>>>> > >>>>> > >>>>> [1] "Error in sampler$call_sampler(args_list[[i]]) : " > >>>>> [2] " c++ exception (unknown reason)" > >>>>> error occurred during calling the sampler; sampling not done > >>>>> > >>>>> I think is a problem with Catalina MacOS, but I don´t know how to > >>> solve it. > >>>>> > >>>>> Manuel > >>>>> > >>>>> -- > >>>>> *Manuel Spínola, Ph.D.* > >>>>> Instituto Internacional en Conservación y Manejo de Vida > >> Silvestre > >>>>> Universidad Nacional > >>>>> Apartado 1350-3000 > >>>>> Heredia > >>>>> COSTA RICA > >>>>> mspin...@una.cr <mspin...@una.ac.cr> > >>>>> mspinol...@gmail.com > >>>>> Teléfono: (506) 8706 - 4662 > >>>>> Personal website: Lobito de río < > >>> https://sites.google.com/site/lobitoderio/> > >>>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> > >>>>> > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> _______________________________________________ > >>>>> R-SIG-Mac mailing list > >>>>> R-SIG-Mac@r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> Manuel Spínola, Ph.D. > >>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre > >>>> Universidad Nacional > >>>> Apartado 1350-3000 > >>>> Heredia > >>>> COSTA RICA > >>>> mspin...@una.cr > >>>> mspinol...@gmail.com > >>>> Teléfono: (506) 8706 - 4662 > >>>> Personal website: Lobito de río > >>>> Institutional website: ICOMVIS > >>> > >>> > >> > >> -- > >> *Manuel Spínola, Ph.D.* > >> Instituto Internacional en Conservación y Manejo de Vida Silvestre > >> Universidad Nacional > >> Apartado 1350-3000 > >> Heredia > >> COSTA RICA > >> mspin...@una.cr <mspin...@una.ac.cr> > >> mspinol...@gmail.com > >> Teléfono: (506) 8706 - 4662 > >> Personal website: Lobito de río < > >> https://sites.google.com/site/lobitoderio/> > >> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-SIG-Mac mailing list > >> R-SIG-Mac@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >> > >> > >> > > > > -- > > *Manuel Spínola, Ph.D.* > > Instituto Internacional en Conservación y Manejo de Vida Silvestre > > Universidad Nacional > > Apartado 1350-3000 > > Heredia > > COSTA RICA > > mspin...@una.cr <mspin...@una.ac.cr> > > mspinol...@gmail.com > > Teléfono: (506) 8706 - 4662 > > Personal website: Lobito de río < > https://sites.google.com/site/lobitoderio/> > > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.cr <mspin...@una.ac.cr> mspinol...@gmail.com Teléfono: (506) 8706 - 4662 Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac