[R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS
Manuel Spínola
m@p|no|@10 @end|ng |rom gm@||@com
Sun Dec 15 00:28:53 CET 2019
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 using 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-bounces using r-project.org on behalf of mspinola10 using 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 (<ken using 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 <mspinola10 using 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 (<ken using 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 <
> mspinola10 using 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
> > > > mspinola using una.cr <mspinola using una.ac.cr>
> > > > mspinola10 using 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 using 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
> > > mspinola using una.cr
> > > mspinola10 using 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
> mspinola using una.cr <mspinola using una.ac.cr>
> mspinola10 using 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 using r-project.org
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>
>
>
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola using una.cr <mspinola using una.ac.cr>
mspinola10 using 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/>
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