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