Error when fitting a brms model, maybe associated with Catalina MacOS
Setting the PATH in the shell does not apply to applications on macOS, e.g. I customize the PATH in my .zshrc, and yet in R.app I have the vanilla PATH:
Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin" RStudio is similar. Gabor On Mon, Dec 16, 2019 at 7:08 PM Simon Urbanek
<simon.urbanek at r-project.org> wrote:
JJB, to be honest, what surprises me is why people don't use the most straight-forward way documented very explicitly in the installer which is simply export PATH=/usr/local/clang7/bin:$PATH I never touch Makevars as that is very error-prone and makes it impossible to use multiple R versions. CRAN is already configured correctly for those compilers so you should not need to do any manual overrides. Cheers, Simon
On Dec 16, 2019, at 1:37 PM, Balamuta, James Joseph <balamut2 at illinois.edu> wrote: Kasper, With all due respect, setting up the ~/.R/Makevars file is a key step that trips up a majority of users. Sadly, the documentation for Makevars is not beginner friendly and is scattered across multiple manuals [1][2] with the most precise explanation being off-site [3]. Moreover, many do not know about R's startup files [4], how to modify them, or where they exist as dot files are hidden by default [5]. I've toyed with many solutions over the years, including but not limited to: providing an R script to write the lines to ~/.R/Makevars, emphasizing that `file.edit()` can be used to open the configuration files, providing step-by-step guides, and so on. The most successful approach taken was to provide as much of an automated process as possible while emphasizing the steps for those who wanted more depth. Having said this, my dream is for the macOS CRAN binary to come with everything configured and setup correctly. Until that is the case or there exists a better approach, I'm more inclined to stick with the current approach I've taken especially as the macOS toolchain's stability changes on minor point releases (MAJOR.MINOR.PATCH). Again, these are made freely available to address an ever clearer need that is arising in the community. Best, JJB [1]: R Installation and Administration, Section 6.3.2: macOS, https://cran.r-project.org/doc/manuals/R-admin.html#macOS-packages [2]: Writing R Extensions, Section 1.2.1: Using Makevars, https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars [3]: StackOverflow, Understanding the contents of the Makevars file in R (macros, variables, ~/.R/Makevars and pkg/src/Makevars), https://stackoverflow.com/q/43597632/1345455 [4]: Initialization at Start of an R Session https://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html [5]: How to Show Hidden Files on a Mac https://www.macrumors.com/how-to/show-hidden-files-on-a-mac/ ?On 12/16/19, 9:39 AM, "R-SIG-Mac on behalf of Kasper Daniel Hansen" <r-sig-mac-bounces at r-project.org on behalf of kasperdanielhansen at gmail.com> wrote: 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 Sp?nola <mspinola10 at 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 s?b., 14 dic. 2019 a las 19:45, Fox, John (<jfox at mcmaster.ca>) escribi?:
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>
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:
Installer Splash:
Post:
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
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
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 <
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> [[alternative HTML version deleted]]
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-- 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]]
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-- *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 <
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/> [[alternative HTML version deleted]]
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-- *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]]
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--
Best,
Kasper
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