Just a comment on the macos-rtools. It seems wrong to me to set the user level ~/.R/Makevars.
On Sat, Dec 14, 2019 at 9:29 PM Manuel Spínola <mspinol...@gmail.com> wrote: > 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 > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
