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 Sp?nola <mspinola10 at gmail.com>
Dear list members,
I updated everything, Catalina, Xcode, CLT, R 3.6.2, rstan from source,
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 =
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
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
is not sufficient as it does not match the prescribed compilation
(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>
An update.
Before doing the suggested installation, I updated Catalina to
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
do these manually.
What it does is described at
On 12 Dec 2019, at 1:14 am, Manuel Sp?nola <mspinola10 at gmail.com>
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>)
What worked for me was installing the tools using
and then installing rstan from source ie
install.packages(?rstan?,type=?source) as suggested on one of the
On 11 Dec 2019, at 11:09 am, Manuel Sp?nola <
Dear list members,
When trying to fit this example from the CRAN repository fro
the following error message after the 4th chain. I am using R
Catalina MacOS.
library(brms)
group <- rep(c("treat", "placebo"), each = 30)
symptom_post <- c(rnorm(30, mean = 1, sd = 2), rnorm(30, mean =
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
Manuel
--
*Manuel Sp?nola, Ph.D.*
Instituto Internacional en Conservaci?n y Manejo de Vida
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 <