Setting the PATH in the shell does not apply to applications on macOS,
e.g. I customize the PATH in my .zshrc, and yet in R.app I have the
vanilla PATH:
> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"RStudio is similar. Gabor On Mon, Dec 16, 2019 at 7:08 PM Simon Urbanek <simon.urba...@r-project.org> wrote: > > JJB, > > to be honest, what surprises me is why people don't use the most > straight-forward way documented very explicitly in the installer which is > simply > > export PATH=/usr/local/clang7/bin:$PATH > > I never touch Makevars as that is very error-prone and makes it impossible to > use multiple R versions. CRAN is already configured correctly for those > compilers so you should not need to do any manual overrides. > > Cheers, > Simon > > > > > On Dec 16, 2019, at 1:37 PM, Balamuta, James Joseph <balam...@illinois.edu> > > wrote: > > > > Kasper, > > > > With all due respect, setting up the ~/.R/Makevars file is a key step that > > trips up a majority of users. Sadly, the documentation for Makevars is not > > beginner friendly and is scattered across multiple manuals [1][2] with the > > most precise explanation being off-site [3]. Moreover, many do not know > > about R's startup files [4], how to modify them, or where they exist as dot > > files are hidden by default [5]. > > > > I've toyed with many solutions over the years, including but not limited > > to: providing an R script to write the lines to ~/.R/Makevars, emphasizing > > that `file.edit()` can be used to open the configuration files, providing > > step-by-step guides, and so on. The most successful approach taken was to > > provide as much of an automated process as possible while emphasizing the > > steps for those who wanted more depth. > > > > Having said this, my dream is for the macOS CRAN binary to come with > > everything configured and setup correctly. Until that is the case or there > > exists a better approach, I'm more inclined to stick with the current > > approach I've taken especially as the macOS toolchain's stability changes > > on minor point releases (MAJOR.MINOR.PATCH). Again, these are made freely > > available to address an ever clearer need that is arising in the community. > > > > Best, > > > > JJB > > > > [1]: R Installation and Administration, Section 6.3.2: macOS, > > https://cran.r-project.org/doc/manuals/R-admin.html#macOS-packages > > [2]: Writing R Extensions, Section 1.2.1: Using Makevars, > > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars > > [3]: StackOverflow, Understanding the contents of the Makevars file in R > > (macros, variables, ~/.R/Makevars and pkg/src/Makevars), > > https://stackoverflow.com/q/43597632/1345455 > > [4]: Initialization at Start of an R Session > > https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html > > [5]: How to Show Hidden Files on a Mac > > https://www.macrumors.com/how-to/show-hidden-files-on-a-mac/ > > > > On 12/16/19, 9:39 AM, "R-SIG-Mac on behalf of Kasper Daniel Hansen" > > <r-sig-mac-boun...@r-project.org on behalf of kasperdanielhan...@gmail.com> > > wrote: > > > > 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 > > > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
