[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 03:28:23 CET 2019 

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 (<jfox using 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 <mspinola10 using 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 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
> >>    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 <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 <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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