[R-SIG-Mac] Error when fitting a brms model, maybe associated with Catalina MacOS

Fox, John j|ox @end|ng |rom mcm@@ter@c@
Sun Dec 15 02:45:47 CET 2019 

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
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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/>
> 
> 	[[alternative HTML version deleted]]
> 
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