Error when fitting a brms model, maybe associated with Catalina MacOS

Did you install rstan last?

Ken

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

)

    > escribi?:

    > > 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 Sp?nola <

mspinola10 at 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 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/>
    > > >
    > > >       [[alternative HTML version deleted]]
    > > >
    > > > _______________________________________________
    > > > R-SIG-Mac mailing list
    > > > R-SIG-Mac at r-project.org
    > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
    > > >

    > >
    > >
    > >
    > > --
    > > 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/>

        [[alternative HTML version deleted]]

--