On 15 Dec 2019, at 10:28 am, Manuel Sp?nola <mspinola10 at 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 (<balamut2 at illinois.edu>) escribi?:
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 Sp?nola" <r-sig-mac-bounces at r-project.org on behalf of mspinola10 at 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 mi?., 11 dic. 2019 a las 16:05, Ken Beath (<ken at kjbeath.com.au>)
escribi?:
> 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 Sp?nola <mspinola10 at gmail.com> wrote:
> >
> > Thank you very much to all.
> >
> > Does Installing the macos-rtools could affect R in other ways?
> >
> > Manuel
> >
> > El mi?., 11 dic. 2019 a las 6:56, Ken Beath (<ken at kjbeath.com.au>)
> > What worked for me was installing the tools using
> >
> > and then installing rstan from source ie
> install.packages(?rstan?,type=?source) as suggested on one of the stan
> forums
> > > On 11 Dec 2019, at 11:09 am, Manuel Sp?nola <mspinola10 at gmail.com>
> > >
> > > Dear list members,
> > >
> > > When trying to fit this example from the CRAN repository fro brms, I
> > > 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
> > > 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
> > >
> > > Manuel
> > >
> > > --
> > > *Manuel Sp?nola, Ph.D.*
> > > Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
> > > Universidad Nacional
> > > Apartado 1350-3000
> > > Heredia
> > > COSTA RICA
> > > mspinola at una.cr <mspinola at una.ac.cr>
> > > mspinola10 at gmail.com
> > > Tel?fono: (506) 8706 - 4662
> > > Personal website: Lobito de r?o <
> >
> >
> >
> > --
> > Manuel Sp?nola, Ph.D.
> > Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
> > Universidad Nacional
> > Apartado 1350-3000
> > Heredia
> > COSTA RICA
> > mspinola at una.cr
> > mspinola10 at gmail.com
> > Tel?fono: (506) 8706 - 4662
> > Personal website: Lobito de r?o
> > Institutional website: ICOMVIS
--
*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Tel?fono: (506) 8706 - 4662
Personal website: Lobito de r?o <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
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