Unserialize(socklist[[1]]) error on Mac Catalina

Interfaces RStan
1

I’m running into the well-known unserialize(socklist[[1]]) error:

Error in unserialize(socklist[[n]]) : error reading from connection

None of the posted fixes have worked for me: I don’t appear to have a Makevars file, so I can’t edit it; I’ve uninstalled and reinstalled everything and rebooted RStudio; I’ve renamed my .stan file to force a re-compile; and I’m running a (very slightly modified version of) one of the case studies posted on the STAN site, so I’m fairly sure it’s not a cockpit error :)

(N.B.: I’ve had this issue across multiple R and .stan files, including an exact copy of a file that runs perfectly on my collaborator’s R installation, but the 8-schools example runs OK.)

Thanks in advance! I’m a bit of an R novice, so hopefully it’s a simple fix.

My R code is here:

`library("splines")
library("rstan")
X <- seq(from=-5, to=5, by=.1) # generating inputs
B <- t(bs(X, knots=seq(-5,5,1), degree=3, intercept = TRUE)) # creating the B-splines
num_data <- length(X); num_basis <- nrow(B)
a0 <- 0.2 # intercept
a <- rnorm(num_basis, 0, 1) # coefficients of B-splines
Y_true <- as.vector(a0*X + a%*%B) # generating the output
Y <- Y_true + rnorm(length(X),0,.2) # adding noise
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())
sm<-stan_model("fit_basis_rename.stan")
fit<-sampling(sm,iter=500,control = list(adapt_delta=0.95),data = list(X=X,Y=Y,B=B,num_data=num_data,num_basis=num_basis))
`

My STAN code is here:

data { 
  int num_data; 
  int num_basis; 
  vector[num_data] Y; 
  vector[num_data] X; 
  matrix[num_basis, num_data] B; 
} 
 
parameters { 
  row_vector[num_basis] a_raw; 
  real a0; 
  real<lower=0> sigma; 
  real<lower=0> tau; 
} 
 
transformed parameters { 
  row_vector[num_basis] a; 
  vector[num_data] Y_hat; 
  a = a_raw*tau;  
  Y_hat = a0*X + to_vector(a*B); 
} 
 
model { 
  a_raw ~ normal(0, 1); 
  tau ~ cauchy(0, 1); 
  sigma ~ cauchy(0, 1); 
  Y ~ normal(Y_hat, sigma); 
}

My OS is macOS Catalina, 10.15.7. I’m running R 4.1.0 and rstan 2.21.2.

The output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars"))) is:
Error: object ‘writeLines(readLines(file.path(Sys.getenv(“HOME”), “.R/Makevars”)))’ not found

I can provide any other information if needed. Thanks again!

2

Hi,
sorry for not getting to you earlier. Do you get any output when running just a single chain in parrallel (e.g setting chains = 1 for sampling)?

3

My R session immediately crashes with the error message “R encountered a fatal error. The session was terminated.” I don’t get any other output.

4

Bad :-( I admit I have no specific idea beyond tagging @andrjohns who’s seen a bunch of those and suggesting trying cmdstanr which tends to be easier to install/maintain: Getting started with CmdStanR • cmdstanr

5

Thanks for the tip! I’ve got CmdStanR up and running as a temporary solution. :)