"The NEXT version of Stan will not be able to pre-process your Stan program."

Summary:

I re-installed my rstan package earlier today, and warning msg starts to show up, and also some models that used to work ok now cannot be run.

Description:

After re-installing rstan, I followed the start guide and checked the following:

pkgbuild::has_build_tools(debug = TRUE)

Somehow it showed FALSE. So I further installed the C++ toolchain using the macOS R toolchain installer.

Now whenever I need to do model fit, I see this message

sh: clang++ -mmacosx-version-min=10.13: command not found
The NEXT version of Stan will not be able to pre-process your Stan program.
Please open an issue at
https://github.com/stan-dev/stanc3/issues
if you can share or at least describe your Stan program. This will help ensure that Stan
continues to work on your Stan programs in the future. Thank you!
This message can be avoided by wrapping your function call inside suppressMessages().
Error in FUN(X[[i]], ...) :
trying to get slot "mode" from an object of a basic class ("NULL") with no slots

And it's usually accompanied with this error msg:

Warning messages:
1: In system2(CXX, args = ARGS) : error in running command
2: In file.remove(c(unprocessed, processed)) :
cannot remove file '/var/folders/fr/b4bvkc_11vj3ntd1r6859x5m0000gn/T//RtmpjkdCOb/file13be45025d82.stan', reason 'No such file or directory'

Sometimes the model can run. Sometimes it failed (whereas previously works ok). And when it fails, in addition to the previous msg, I also got the following one:

3: In mccollect(jobs) : 2 parallel jobs did not deliver results

Reproducible

Here's the codes I was using where it fails to run:

stan file (filename:lab-02-nopool.stan) :

data { 
  int<lower=0> n;           // items 
  int<lower=0> N[n];        // initial trials 
  int<lower=0> y[n];        // initial successes 
  real<lower = 0> a;        // beta param1
  real<lower = 0> b;        // beta param2
} 
parameters { 
  vector<lower=0, upper=1>[n] theta;  // chance of success (unpooled) 
} 
model { 
  y ~ binomial(N, theta);  // likelihood 
  theta ~ beta(a,b);
}

R code

tumors <- read.csv(file = url("http://www.stat.columbia.edu/~gelman/book/data/rats.asc"),
                     skip = 2, header = T, sep = " ")[,c(1,2)]
y <- tumors$y
N <- tumors$N
n <- length(y)

stan_dat <- list(n = n, N = N, y =y, a = 1, b = 1)
fit_nopool <- stan('lab-02-nopool.stan', data = stan_dat, chains = 2, refresh = 0)
nopool_output <- rstan::extract(fit_nopool)

Here's info on my systems:

RStan Version:

2.21.1

R Version:

R 4.0.1

Operating System:

macOS Catalina 10.15.5

Start with the supplied pkgbuild::has_build_tools(debug = TRUE) check and the stan('lab-02-nopool.stan', ...) call using the included R code on macOS Catalina. Investigate the reported clang++ command-not-found and confirm that the Stan model compiles and runs without the intermittent errors; the issue does not identify a repository file or test to change.