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

Kasper Daniel Hansen k@@perd@n|e|h@n@en @end|ng |rom gm@||@com
Mon Dec 16 16:38:48 CET 2019 

Just a comment on the macos-rtools. It seems wrong to me to set the user
level ~/.R/Makevars.

On Sat, Dec 14, 2019 at 9:29 PM Manuel Spínola <mspinola10 using gmail.com> wrote:

> 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/>
>
>         [[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
>


-- 
Best,
Kasper

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